GATK

Tagged with #strand-bias
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Explanation of strand bias detected in GATK

Hi,

I have seen the definition of strand bias on this site (below) but I need a little clarification. Does the FS filter (a) highlight instances where reads are only present on a single strand and contain a variant (as may occur toward the end of exome capture regions) or does it (b) specifically look for instances where there are reads on both strands but the variant allele is disproportionately represented on one strand (as might be indicative of a false positive), or does it (c) do both?

I had thought it did (b) but have encountered some disagreement.

** How much evidence is there for Strand Bias (the variation being seen on only the forward or only the reverse strand) in the reads? Higher SB values denote more bias (and therefore are more likely to indicate false positive calls.

Strand Bias (SB) value

All,

The Strand Bias (SB) value on the vcf file looks so difference from the gatk1.5 & 2.1 1. On the gatk 1.5, SB=0 or 0.1 is acceptable, the smaller SB the better ... etc 2. On gatk 2.1 SB~-6.1e03 ???

My question is what is cut-off SB value (acceptable!)

Thanks, Q

UnifiedGenotyper / Strand Bias (SB)

Hi,

How to get all SNPs variants with Strand Bias (high SB value) ?

GenomeAnalysisTK.jar -T UnifiedGenotyper  \
    -R  ucsc.hg19.fasta   -D dbsnp_135.hg19.vcf  \
    -stand_emit_conf 1.5 -stand_call_conf 1.5 \
    -o Sample_2.snv.vcf  -I Sample_2.recal.bam -nt 10

Thanks, Q