UnifiedGenotyper / Strand Bias (SB)
Posted in Ask the GATK team | Last updated on 2013-01-07 20:31:53


Comments (7)

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


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