Dear members,
I am using the mpileup tool as described at
http://samtools.sourceforge.net/mpileup.shtml
samtools mpileup -ugf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFiler -Q20 -d10 > var.flt.vcf
I do not understand options used:
1. at first line flags "-ugf" are used. The meaning (according to manual) is:
-g Compute genotype likelihoods and output them in the binary call format (BCF).
-u Similar to -g except that the output is uncompressed BCF, which is preferred for piping.
If so, why using "-u" and "-g" together?
2. At the second line, I used flags -Q20 to filter out QUAL less than 20. However, in the generated VCF file I found lots of variants (about 1000 out of 22000 total) with QUAL less than 20.
Any one could explain?
Thank you very much in advance
Vlad:
I am using the mpileup tool as described at
http://samtools.sourceforge.net/mpileup.shtml
samtools mpileup -ugf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFiler -Q20 -d10 > var.flt.vcf
I do not understand options used:
1. at first line flags "-ugf" are used. The meaning (according to manual) is:
-g Compute genotype likelihoods and output them in the binary call format (BCF).
-u Similar to -g except that the output is uncompressed BCF, which is preferred for piping.
If so, why using "-u" and "-g" together?
2. At the second line, I used flags -Q20 to filter out QUAL less than 20. However, in the generated VCF file I found lots of variants (about 1000 out of 22000 total) with QUAL less than 20.
Any one could explain?
Thank you very much in advance
Vlad: