I generated a file using the command:
"samtools mpileup -m 1796 -ugf ref.fa raw.bam > raw.mpileup.output"
it worked fine. Then I tried to use bcftools to generate vcf file using:
"bcftools view -bvcg raw.mpileup.output | bcftools view - > test.var.raw.vcf".
The first lines on screen looked fine for me and the output file test.var.raw.vvf keeps increasing:
[bcfview] 100000 sites processed.
[afs] 0:99821.109 1:147.549 2:31.342
[bcfview] 200000 sites processed.
[afs] 0:99882.002 1:105.096 2:12.902
However from certain site on (I checked and it seems to be on chr1) it turned out to be this:
[bcfview] 150600000 sites processed.
[afs] 0:100000.000 1:0.000 2:0.000
[bcfview] 150700000 sites processed.
[afs] 0:100000.000 1:0.000 2:0.000
[bcfview] 150800000 sites processed.
[afs] 0:100000.000 1:0.000 2:0.000
and the output file, test.var.raw.vcf, was no longer changed.
Does anyone know where is wrong or did I miss something in the command line?
Thank you! Any suggestion would be greatly appreciated....
"samtools mpileup -m 1796 -ugf ref.fa raw.bam > raw.mpileup.output"
it worked fine. Then I tried to use bcftools to generate vcf file using:
"bcftools view -bvcg raw.mpileup.output | bcftools view - > test.var.raw.vcf".
The first lines on screen looked fine for me and the output file test.var.raw.vvf keeps increasing:
[bcfview] 100000 sites processed.
[afs] 0:99821.109 1:147.549 2:31.342
[bcfview] 200000 sites processed.
[afs] 0:99882.002 1:105.096 2:12.902
However from certain site on (I checked and it seems to be on chr1) it turned out to be this:
[bcfview] 150600000 sites processed.
[afs] 0:100000.000 1:0.000 2:0.000
[bcfview] 150700000 sites processed.
[afs] 0:100000.000 1:0.000 2:0.000
[bcfview] 150800000 sites processed.
[afs] 0:100000.000 1:0.000 2:0.000
and the output file, test.var.raw.vcf, was no longer changed.
Does anyone know where is wrong or did I miss something in the command line?
Thank you! Any suggestion would be greatly appreciated....
Comment