Error in VCF format ?

[atourneu]

I have generated a VCF using BCFtools on CentOS 7. When calling Vartrix, this VCF is not recognized :
Vartrix error. v1.1.14.
Error: failed to open BCF/VCF from /home/ulb/iribhm/atourneu/variant/ATC_merged.vcf

stack backtrace:
0: failure::backtrace::Backtrace::new
at /root/.cargo/registry/src/github.com-1ecc6299db9ec823/failure-0.1.5/src/backtrace/internal.rs:44
<failure::backtrace::Backtrace as core::default::Default>::default
at /root/.cargo/registry/src/github.com-1ecc6299db9ec823/failure-0.1.5/src/backtrace/mod.rs:125
1: vartrix::_main
at /root/.cargo/registry/src/github.com-1ecc6299db9ec823/failure-0.1.5/src/error/error_impl.rs:19
2: vartrix::main
at src/main.rs:154
3: std::rt::lang_start::{{closure}}
at /rustc/b8cedc00407a4c56a3bda1ed605c6fc166655447/src/libstd/rt.rs:67
4: main
5: __libc_start_main
6:

If you think this is bug in Vartrix, please file a bug at https://github.com/10xGenomics/vartrix, and include the information above and the command-line you used.

Command line used :
vartrix_linux -v $wdi/ATC_merged.vcf -b $tmp/atc2sn1.bam -f $tmp/genome.fa -c $tmp/atc2sn1.tsv -o $wdi/vartrix --threads $ncores

[pmarks]

@atourneu my apologies for the delay. Are you still having this issue? If so, can you post the header & first few lines of your VCF?

[Cathy94]

@atourneu my apologies for the delay. Are you still having this issue? If so, can you post the header & first few lines of your VCF?

I also met this problem, this is my VCF:
##version gdc-1.0.0
##fileDate 20170929
##annotation_spec gdc-1.0.1-public
##n.anlyzed.samples 986
##tumor.aliquots_submitter_id T150
#CHROM POS REF ALT SAMPLE GENE TYPE QUAL FILTER INFO
10 46998995 C G T150 GPRIN2 missense_variant . . depth=20
19 55494632 A G T150 NLRP2 inframe_deletion . . depth=20
19 50435749 A AC T150 ATF5 frameshift_variant . . depth=20
2 189876400 G T T150 COL3A1 missense_variant . . depth=20

[pmarks]

@Cathy94 can you please post the full error message you recieved? Can you also please check what version of vartrix you are using? vartrix -v should tell you. If you're using a version earlier that 1.1.22, please update as we've fixed various issues. You can download the latest release here: https://github.com/10XGenomics/vartrix/releases/tag/v1.1.22