Samtools vcf file filtering
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7 days ago

Hi, I am using samtools inbuilt https://github.com/lh3/samtools/blob/master/bcftools/vcfutils.pl to filter my vcf file. So before setting up my parameters, I wanted to know what is the default value set in the script for these options:

Options:

-Q INT minimum RMS mapping quality for SNPs [$opts{Q}]

     -d INT    minimum read depth [$opts{d}]

   -D INT    maximum read depth [$opts{D}]

     -a INT    minimum number of alternate bases [$opts{a}]

   -w INT    SNP within INT bp around a gap to be filtered [$opts{w}]

   -W INT    window size for filtering adjacent gaps [$opts{W}]

   -1 FLOAT  min P-value for strand bias (given PV4) [$opts{1}]

   -2 FLOAT  min P-value for baseQ bias [$opts{2}]

   -3 FLOAT  min P-value for mapQ bias [$opts{3}]

   -4 FLOAT  min P-value for end distance bias [$opts{4}]

     -e FLOAT  min P-value for HWE (plus F<0) [$opts{e}]

   -p        print filtered variants

Thank you!

samtools RNAseq sequencing • 54 views
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