Question: repeat BQSR and Indel realign
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gravatar for zhou
2.4 years ago by
zhou0
zhou0 wrote:

Dear all, I copied bam files of tumor-normal pairs from others and conducted base quality recalibration and indel realign according to GATK best practice. Then I called variants by UnifiedGenotyper,followed by some filters.However,I found the bams had been handled with BQSR and Indelrealign by my colleagues. So many faults for the first analysis! I would like to know the effect of repeated BQSR and realign on variant calling and false positive rate?

Many thanks!
snp bam • 749 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by zhou0
0
gravatar for zhou
2.4 years ago by
zhou0
zhou0 wrote:

Today I did variant calling with the original bams again and compared two vcfs. The number of variants in two vcfs is similar. QUALs in vcf with repeated BQSR and indel realign are slightly smaller than those in another vcf for the same snp.But for indels,the situation seems to be opposite. Does anyone tell the reason?

Many thanks!

ADD COMMENTlink written 2.4 years ago by zhou0
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