Hi, I got some candidate SNVs by samtools mpileup (command: samtools mpileup -B -Q 13 -q 10 -d 1000000 -f hg19.fasta merged.bam -l bed1.bed). For support by super-high depth, I found a large number of candidate SNVs by analysis the pileup-result. However, there are large number of false positives, and I got these info including depth, Allele frequency, strand bias and average base quality for each site. Could you have any suggest about filteration for false positives? Or is there any tools in samtools to get a value for evaluation, just like VQ in GATK(VQSR)? Thank you. Looking forwad to your reply.
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