to call snp and indels, in FAQ of samtools , it gives
samtools pileup -vcf ref.fa aln.bam | tee raw.txt | samtools.pl varFilter -D100 > flt.txt
awk '($3=="*"&&$6>=50)||($3!="*"&&$6>=20)' flt.txt > final.txt
why use -D and how to determine it
i think the higer depth, mutation will be more credible.
samtools pileup -vcf ref.fa aln.bam | tee raw.txt | samtools.pl varFilter -D100 > flt.txt
awk '($3=="*"&&$6>=50)||($3!="*"&&$6>=20)' flt.txt > final.txt
why use -D and how to determine it
i think the higer depth, mutation will be more credible.
