Hi Admin,
I run samtools mpileup using the following parameters.
samtools mpileup -B -q 1 -f $ref -l $bedFile $3/$4_Tumor.sorted.bam >
$3/$4_Tumor.pileup
I found that the pileup file also the eventual vcf has variants in
positions not in the bed file. There are around 30 such variants out of the
7500 variants called. Can you please tell me if this is a bug or if it is
normal to see variants in non-bed regions.
Thanks and Regards,
Pramod
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