I am stuck with concluding a variant call I made on two BAM files (two samples).
Say sample1 and sample 2 for a specific region.
The command I used:
samtools mpileup -uf hg19.fa sample1.bam sample2.bam -r Chromosomal_Region | bcftools view -bvcg - > var.raw.bcf bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf
I get a result which looks like this:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sampl2 chrxyz 74311283 0 A G 4.61 0 DP=2;VDB=0.0465;AF1=1;AC1=4;DP4=0,0,0,2;MQ=37;FQ=-28.7 GT:PL:DP:GQ 0/1:0,0,0:0:3 1/1:34,6,0:2:4 chrxyz 74311467 0 G A 70.2 0 DP=3;VDB=0.0442;AF1=1;AC1=4;DP4=0,0,3,0;MQ=37;FQ=-32.3 GT:PL:DP:GQ 1/1:67,6,0:2:12 1/1:37,3,0:1:9
please ignore the value in chromosome column. In filter column it gave me 0, I don't know if it can be trusted or trashed? My gut feeling and my limited knowledge in SNP calling suggests me to take the second SNP and follow it up with the variant_effect_predictor from ensembl.
Any help in describing the results mentioned here will be appreciated and also suggestion for further analysis are also welcome (like insilico analysing these variants).