SE sequencing

renamed umi modules

new hapcal

filters for varscan as variables

sorting script name corrected

sorting incorporated into umi and dedup

sorting removed

main for UMI

HC best practices

uniformity

on-target reads

lower avg qual imit

compression level 1

varscan filters returned

HsMetrics

read pandas on closed file

correct id

Merge branch 'master' of https://gitverse.ru/d_bug/BashGATK

ubam work in umi

ubam before umi

quit on error

ubam work in umi

bwa commands, fgbio parameters

bwa commands

Merge branch 'master' of https://gitverse.ru/d_bug/BashGATK

qc with fastp

update annovar omitted

Merge branch 'master' of https://gitverse.ru/sc/d_bug/BashGATK

temp_id corrected