I'm working with matched tumor-normal samples and I want to call somatic variants using Somatic Sniper.
So far I got the main function working with
bam-somaticsniper -Q 40 -G -L -f genome/hg19.fa Results/kayrotypicT.bam Results/kayrotypicN.bam SomSniperResults.txt
and now I need to filter the results.
first question is:
the SomaticSniper guide says explicitly NOT to use mpileup,
You will also need to generate a samtools pileup (not mpileup) indel file.
so, an old post explains the difference..while I think samtools replaced pileup with mpileup, so, since mpileup should output pileup still, is mpileup fine then?
since the example uses a -vcf output I'm creating the pileup and doing the filtering in the following way
# create pileup file samtools mpileup -A -B -vuf genomes/hg19.fa Results/kayrotypic.bam > SomSniperResults/var.raw.pileup
a snapshot of my output looks like this:
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RS-01926692_JC590_RS-01925823 chr1 10008 . A <X> 0 . DP=1;I16=0,1,0,0,33,1089,0,0,0,0,0,0,0,0,0,0;QS=1,0;MQ0F=1 PL 0,3,4 chr1 10009 . A <X> 0 . DP=1;I16=0,1,0,0,30,900,0,0,0,0,0,0,1,1,0,0;QS=1,0;MQ0F=1 PL 0,3,4 chr1 10010 . C <X> 0 . DP=1;I16=0,1,0,0,33,1089,0,0,0,0,0,0,2,4,0,0;QS=1,0;MQ0F=1 PL 0,3,4
however, when i call
samtools.pl varFilter test.pileup | awk '$6>=20'
I get the following error:
Argument "DP=1;I16=0,1,0,0,33,1089,0,0,0,0,0,0,0,0,0,0;QS=1,0;MQ0F=1" isn't numeric in numeric lt (<) at samtools.pl line 117, <> line .
which comes from the fact that the 7th column should be numeric while what I have is the info from the vcf file...
I also tried not to output a vcf file and tried to use bcftools as:
samtools mpileup -A -B -guf /genomes/hg19.fa chr20_bam.bam > test.pileup bcftools/bcftools view -Hgc test.pileup [bcf_sync] incorrect number of fields (0 != 5) at 0:0
I looked at the post here but it didn't solve my problem since i'm not piping and I am testing only one small chr (chr20) from the bam file
so I'm not totally sure how to get it to work.
-- txt was edited with some updated info --