Samtools Version (0.1.18) error: I called SNPs for 17 samples from same organism, however some of the samples failed to list any SNPs on some of the chromosomes even though I expected some SNPs. Hence I looked in IGV browser and pileup information in order to verify whether there are any alternate alleles at the base position. It was clear that these positions had all mapped reads with alternate bases as compared to reference bases.
I removed –v option from bcftools commands to get depth information for all the base positions irrespective of being called variant sites.
Here is the command I used
samtools mpileup -6 -Buf ../gff_and_Refgenome/ref.fasta in.bam | bcftools view -bcg -> in.var.raw.bcf
bcftools view in.var.raw.bcf > vcfutils.pl varFilter -D50 > in.var.fil.vcf
which gave following result for one of probable SNP positions, failed to be listed as SNP (AtoT) in final result file.
Chr2 617743 . A . 28.2 . DP=95;VDB=0.0535;;AC1=2;FQ=-30 PL 0
I would really appreciate if anyone would help me understand why such SNPs were ignored in final file eventhough it display VDB values which are related to SNP calling in samtools.
I removed –v option from bcftools commands to get depth information for all the base positions irrespective of being called variant sites.
Here is the command I used
samtools mpileup -6 -Buf ../gff_and_Refgenome/ref.fasta in.bam | bcftools view -bcg -> in.var.raw.bcf
bcftools view in.var.raw.bcf > vcfutils.pl varFilter -D50 > in.var.fil.vcf
which gave following result for one of probable SNP positions, failed to be listed as SNP (AtoT) in final result file.
Chr2 617743 . A . 28.2 . DP=95;VDB=0.0535;;AC1=2;FQ=-30 PL 0
I would really appreciate if anyone would help me understand why such SNPs were ignored in final file eventhough it display VDB values which are related to SNP calling in samtools.
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