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12 Open 0 Closed
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Issues list

Liftovered b37 to hg19 somatic PON resource
#18 opened Mar 5, 2020 by cgpu
Replace FASTQC with fastp
#15 opened Jan 3, 2020 by cgpu
seed length
#14 opened Jan 3, 2020 by cgpu
Safely split reads
#13 opened Jan 3, 2020 by cgpu
1 task
FASTQ to uBAM takes a long time! (5hours)
#12 opened Jan 1, 2020 by cgpu
bed file vs intervals coordinate system
#11 opened Dec 31, 2019 by cgpu
HapCall: Consider adding -forceActive and -dontTrimActiveRegions simultaneously to reduce false negatives
#10 opened Dec 30, 2019 by cgpu
:caution: "HaplotypeCaller does not call variant depending on the interval list I use"
#9 opened Dec 30, 2019 by cgpu
MarkDuplicatesSpark: consider adding --conf 'spark.local.dir=./tmp
#6 opened Dec 9, 2019 by cgpu
Benchmark execution time + cost of using EstimateLibraryComplexity seperately instead of writing a metrics file in MarkDuplicatesSpark
#5 opened Dec 8, 2019 by cgpu
MarkDuplicateSpark is slower than normal MarkDuplicates - solution: omit -M
#4 opened Dec 8, 2019 by cgpu
bwa mem | samtools sort hybrid command introduces inefficiency ( up to 3x longer runtime)
#3 opened Dec 4, 2019 by cgpu
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