Question: Samtools Options Issues - Mpileup -I With Vcfutils.Pl Varfilter -W ???
0
gravatar for BWilson
7.1 years ago by
BWilson0
BWilson0 wrote:

I am having an issue with samtools that I wondered if you might know. I have been using samtools to call snps using a .bam file which I also created using samtools. I was only interested in snps and not indels, so I used the -I option in mpileup, in addition I was hoping to filter the snps using "vcfutils.pl varfilter -w 1000" in order to filter out an snps within 1kb of a gap.

The issue, however, is that I only seem to be able to use one option or the other. That is, if I use -I to eliminate indels, then I can not use "-w 1000" to filter them, and I end up with the same number of snps (in fact the same file) no matter what value is used for -w. However, when I do not use the -I option, then I end up with a much smaller number of snps when using "-w 1000."

I have provided the commands below:

"-I -w1000" --> 26,395 snps ( results in same file as immediately below)

samtools mpileup -ugf referenceGenome.fasta sortedIndexed.bam -r Gm02:1000000-15000000 -E -S -C 60 -D -d 10000 -I | bcftools view -Nbcvg - > tmp.bcf

bcftools view tmp.bcf | vcfutils.pl varFilter -d 8 -D 100 -w 1000 - > result.vcf

"-I -w100" --> 26,395 snps ( results in same file as immediately above)

samtools mpileup -ugf referenceGenome.fasta sortedIndexed.bam -r Gm02:1000000-15000000 -E -S -C 60 -D -d 10000 -I | bcftools view -Nbcvg - > tmp.bcf

bcftools view tmp.bcf | vcfutils.pl varFilter -d 8 -D 100 -w 100 - > result.vcf

"-w1000" --> 7,444 snps

samtools mpileup -ugf referenceGenome.fasta sortedIndexed.bam -r Gm02:1000000-15000000 -E -S -C 60 -D -d 10000 | bcftools view -Nbcvg - > tmp.bcf

bcftools view tmp.bcf | vcfutils.pl varFilter -d 8 -D 100 -w 1000 - > result.vcf

"-w100" --> 22,001 snps

samtools mpileup -ugf referenceGenome.fasta sortedIndexed.bam -r Gm02:1000000-15000000 -E -S -C 60 -D -d 10000 | bcftools view -Nbcvg - > tmp.bcf

bcftools view tmp.bcf | vcfutils.pl varFilter -d 8 -D 100 -w 100 - > result.vcf

Does anyone know if mpileup -I an varFilter -w are incompatible?

samtools • 3.3k views
ADD COMMENTlink written 7.1 years ago by BWilson0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 829 users visited in the last hour