Retain read names in mpileup and VarScan
I'm looking for mutations in tumor samples by making samtools mpileup with the reference genome, the tumor and the normal aligned/sorted/marked BAM files and then calling variants with VarScan somatic mpileup option. Is it possible to retain in the VarScan output SNP (and INDEL) file the read names from the tumor sample that support the variant call? If VarScan doesn't allow retaining read names, is it possible to make an mpileup file (either with samtools or with bcftools) in which tumor read names would be retained?
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vasily.dobrovolsky •
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