Publish Version III of the SNP+TR reference haplotype panel

README.md

@@ -79,6 +79,10 @@ statSTR --vcf EnsembleTR_file.vcf.gz
         --out EnsembleTR_per_locus_allele_frequency
 ```
 
+# EnsembleTR data releases
+
+Archived datasets, including the Version II calls and other versions of haplotype panel files can be found [here](archive_ensembletr_datasets.md).
+
 ## Version II of EnsembleTR calls on samples from 1000 Genomes Project and H3Africa
 
 Chromosome 1 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/add-vntrs/ensemble_chr1_filtered.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/add-vntrs/ensemble_chr1_filtered.vcf.gz.tbi)
@@ -125,76 +129,86 @@ Chromosome 21 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/add-vntr
 
 Chromosome 22 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/add-vntrs/ensemble_chr22_filtered.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/add-vntrs/ensemble_chr22_filtered.vcf.gz.tbi)
 
-## Version II of reference SNP+TR haplotype panel for imputation of TR variants
+## Version IV of reference SNP+TR haplotype panel for imputation of TR variants
 
-### Dataset description
+These files contain:
+* [Phased SNP and indel variants](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/) of 3,202 samples from the 1000 Genomes Project (1kGP).
+* TRs phased/imputed from 3,202 1kGP samples based on EnsembleTR calls.
 
-[Phased variants](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/) of 3,202 samples from the 1000 Genomes Project (1kGP).
+There are in total 1,070,762 TRs and 70,692,015 SNPs/indels.
 
-TRs imputed from 3,202 1kGP samples.
+All the coordinates are based on **hg38** human reference genome.
 
-Total 70,692,015 variants + 1,091,550 TR markers.
+These files contain the same data as [Version II](archive_ensembletr_datasets.md), with the following updates to facilitate use in downstream imputation pipelines:
 
-All the coordinates are based on **hg38** human reference genome.
+1. Remove TRs for which the REF allele does not match the expected sequence based on CHR:POS
+2. For each TR, remove alelles with 0 count.
+    * If reference allele have 0 count, keep the reference alleles.
+3. Remove TRs which have more than 100 alleles.
+4. Remove TRs which have less than 2 alleles.
+5. Remove the DS/GP fields which are large and not used by downstream steps.
+6. Add unique IDs for each TR of the format EnsTR:CHROM:POS. For TRs with the same CHR:POS, add the duplicate number of the TR following format: EnsTR:CHROM:POS:Duplicate_num. Duplicated loci with identical alleles are removed.
+7. Add VT field, set to VT=TR for TRs and VT=OTHER for other variant types
+8. Add the bref format files which have the same information as the VCFs but can improve Beagle imputation performance.
 
-### Availability
+All file description and download links can be found [here](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_4_readme.txt). Data and links for each chromosome for the Verson IV panel are also provided below. 
 
-Chromosome 1 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr1_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr1_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 1 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr1.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr1.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr1.bref3)] SNPs/indels=5,759,060 TRs=92,378
 
-Chromosome 2 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr2_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr2_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 2 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr2.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr2.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr2.bref3)] SNPs/indels=6,088,598 TRs=91,137
 
-Chromosome 3 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr3_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr3_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 3 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr3.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr3.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr3.bref3)] SNPs/indels=4,983,185 TRs=75,243
 
-Chromosome 4 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr4_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr4_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 4 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr4.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr4.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr4.bref3)] SNPs/indels=4,875,465 TRs=69,327
 
-Chromosome 5 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr5_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr5_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 5 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr5.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr5.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr5.bref3)] SNPs/indels=4,536,819 TRs=66,492
 
-Chromosome 6 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr6_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr6_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 6 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr6.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr6.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr6.bref3)] SNPs/indels=4,315,217 TRs=65,940
 
-Chromosome 7 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr7_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr7_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 7 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr7.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr7.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr7.bref3)] SNPs/indels=4,137,254 TRs=59,422
 
-Chromosome 8 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr8_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr8_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 8 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr8.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr8.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr8.bref3)] SNPs/indels=3,886,222 TRs=55,144
 
-Chromosome 9 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr9_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr9_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 9 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr9.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr9.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr9.bref3)] SNPs/indels=3,165,513 TRs=44,189
 
-Chromosome 10 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr10_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr10_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 10 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr10.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr10.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr10.bref3)] SNPs/indels=3,495,473 TRs=51,640
 
-Chromosome 11 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr11_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr11_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 11 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr11.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr11.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr11.bref3)] SNPs/indels=3,423,341 TRs=49,603
 
-Chromosome 12 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr12_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr12_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 12 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr12.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr12.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr12.bref3)] SNPs/indels=3,332,788 TRs=55,887
 
-Chromosome 13 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr13_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr13_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 13 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr13.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr13.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr13.bref3)] SNPs/indels=2,509,179 TRs=35,720
 
-Chromosome 14 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr14_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr14_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 14 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr14.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr14.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr14.bref3)] SNPs/indels=2,290,400 TRs=36,203
 
-Chromosome 15 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr15_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr15_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 15 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr15.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr15.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr15.bref3)] SNPs/indels=2,109,285 TRs=32,338
 
-Chromosome 16 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr16_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr16_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 16 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr16.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr16.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr16.bref3)] SNPs/indels=2,362,361 TRs=35,452
 
-Chromosome 17 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr17_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr17_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 17 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr17.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr17.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr17.bref3)] SNPs/indels=2,073,624 TRs=38,382
 
-Chromosome 18 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr18_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr18_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 18 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr18.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr18.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr18.bref3)] SNPs/indels=1,963,845 TRs=28,446
 
-Chromosome 19 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr19_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr19_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 19 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr19.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr19.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr19.bref3)] SNPs/indels=1,670,692 TRs=33,536
 
-Chromosome 20 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr20_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr20_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 20 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr20.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr20.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr20.bref3)] SNPs/indels=1,644,384 TRs=25,745
 
-Chromosome 21 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr21_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr21_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 21 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr21.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr21.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr21.bref3)] SNPs/indels=1,002,753 TRs=12,894
 
-Chromosome 22 [VCF file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr22_final_SNP_merged_additional_TRs.vcf.gz) and [tbi file](https://ensemble-tr.s3.us-east-2.amazonaws.com/additional-phased-trs/chr22_final_SNP_merged_additional_TRs.vcf.gz.tbi)
+Chromosome 22 [[VCF](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr22.vcf.gz)] [[tbi](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr22.vcf.gz.tbi)] [[bref](https://ensemble-tr.s3.us-east-2.amazonaws.com/ensembletr-refpanel-v4/ensembletr_refpanel_v4_chr22.bref3)] SNPs/indels=1,066,557 TRs=15,644
 
 ### Usage
 
 Use [Beagle](https://faculty.washington.edu/browning/beagle/beagle.html) to impute TRs into SNP data:
 
 ```
 java -Xmx4g -jar beagle.version.jar \
-            gt=SNPs.vcf.gz \
-            ref=${chrom}_final_SNP_merged.vcf.gz \
-            out=imputed_TR_SNPs
+            gt=SNPs_chr${chrom}.vcf.gz \
+            ref=ensembletr_refpanel_v4_chr${chrom}.bref3 \
+            out=imputed_TR_SNPs_chr${chrom}
 ```
 
-Please use the [version 5.4](https://github.com/gymreklab/1000Genomes-TR-Analysis/raw/main/phasing/validation/beagle.19Apr22.7c0.jar) for this analysis as we had issues with the newer versions of Beagle and we are right now communicating it with Beagle developers.
+We have tested this with Beagle jar file [beagle.27May24.118.jar](https://faculty.washington.edu/browning/beagle/beagle.27May24.118.jar). Earlier releases of Beagle 5.4 had problems imputing from this panel due to a file decompression issue.
 
 ## Additional resources
 
@@ -203,14 +217,6 @@ Per locus summary statistics can be downloaded from [here](https://ensemble-tr.s
 Population-specific per locus statistics on allele frequency, heterozygosity, and the number of called samples can be found [here](https://ensemble-tr.s3.us-east-2.amazonaws.com/tables/afreq_tables.zip). Statistics are computed using statSTR from the TRTools package.
 
 
-## Version I
-
-For version I of EnsembleTR calls, please use 
-https://ensemble-tr.s3.us-east-2.amazonaws.com/split/ensemble_chr"$chr"_filtered.vcf.gz for VCF file and https://ensemble-tr.s3.us-east-2.amazonaws.com/split/ensemble_chr"$chr"_filtered.vcf.gz.tbi for tbi file.
-
-For version I of phased panels, please use 
-https://ensemble-tr.s3.us-east-2.amazonaws.com/phased-split/chr"$chr"_final_SNP_merged.vcf.gz for VCF file and https://ensemble-tr.s3.us-east-2.amazonaws.com/phased-split/chr"$chr"_final_SNP_merged.vcf.gz.csi for tbi file.
-
 ## Notes on HipSTR input
 
 HipSTR might expand the coordinates of the repeat if there is a nearby SNP. If you have multiple HipSTR outputs from different individuals and want to use mergeSTR to merge them, please use our python script, *Hipstr_correction.py*, to correct the merged HipSTR VCF file ensuring that multiple records from the same repeat culminate in a single unified record.