Hello,
I'm using samtools and bcftools to call snps from a targeted resequencing project. Nucleotide polymorphisms seem to be fine, but indels are proving to be a problem. I can see the indels in, say, samtools tview, with high coverage. However, my samtools/bcftools output find only a few reads at the relevant position.
My commands (following local realignment) are:
samtools mpileup -uf concatenated.fasta -L 1000000 -d 1000000 Ec_A10.realigned.bam >Ec_A10.mpileup
bcftools view -bvc Ec_A10.mpileup >Ec_A10.var.raw.bcf
bcftools view Ec_A10.var.raw.bcf >Ec_A10_name.vars.tsv
The relevant line from the output is:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Ec_A10.test
concatenated 2000 . CATCCTCGATGT C 185 . INDEL;DP=9;VDB=0.0074;AF1=0.5;AC1=1;DP4=2,2,1,4;MQ=60;FQ=159;PV4=0.52,0.00017,1,1 PL 223,0,194
So, what is strange is that the reported depth is 9 reads, but there are clearly many more - I've also attached a screen shot from tview. Any suggestions on how to clear this up?
Thanks!
I'm using samtools and bcftools to call snps from a targeted resequencing project. Nucleotide polymorphisms seem to be fine, but indels are proving to be a problem. I can see the indels in, say, samtools tview, with high coverage. However, my samtools/bcftools output find only a few reads at the relevant position.
My commands (following local realignment) are:
samtools mpileup -uf concatenated.fasta -L 1000000 -d 1000000 Ec_A10.realigned.bam >Ec_A10.mpileup
bcftools view -bvc Ec_A10.mpileup >Ec_A10.var.raw.bcf
bcftools view Ec_A10.var.raw.bcf >Ec_A10_name.vars.tsv
The relevant line from the output is:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Ec_A10.test
concatenated 2000 . CATCCTCGATGT C 185 . INDEL;DP=9;VDB=0.0074;AF1=0.5;AC1=1;DP4=2,2,1,4;MQ=60;FQ=159;PV4=0.52,0.00017,1,1 PL 223,0,194
So, what is strange is that the reported depth is 9 reads, but there are clearly many more - I've also attached a screen shot from tview. Any suggestions on how to clear this up?
Thanks!
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