I will try to wrap everything up in a single post so my apologies for being not accurate in the title. First of all, i would like to mention that I have read following previously asked questions. So I am not asking without any background checking.
My aim is to filter my vcf files from known dbsnp and homozygous mutations to eliminate false positives. My data comes from ICGC so I believe its quality is pretty good. I will filtering process fro same patients vcf from multiple centers, then i will merge them.
While I was working on pindel indel vcf, the genotype information was stated as "./." . In the first link that I have referred, It was mentioned that this "./." is related with no genotype information. When I checked all mutations rows, GT was "./.". In order to filter out homozygous mutations, what should I do ? Shouldn't there be a information such as "1/1" like I had in all of my SNV vcfs.
For filtration in SNV vcf, I used snpEff. Will snpEff change the found mutations in a default run ? But it seems like it did not change anything. Should I use snpsift ? Could you also tell me is there any difference between vcftools and snpsift. (they seem to serve for the same purpose)
I may need some help about understanding some terminology in the vcf header.
In my indel vcf, one of the filter is below. Could you tell me the difference in the given two mutations. What does it mean if F012 is under FILTER column. Will that mean mutationA has that specific filter property or does not have. Could you illuminate me in this terminology?
##FILTER=<ID=F012,Description="Germline: When length < 11 and depth > 9, fail if the variant is seen in both 20% of normal reads AND 20% of tumour reads in either pindel or bwa" A 1 13656 ef9c648a-206e-11e5-a9d9-adff273a0828 CAG C 78 F016;F010;F015 PC=D;RS=13656;RE=13659;LEN=2;S1=12;S2=270.339;REP=1;F017 GT:PP:NP:PB:NB:PD:ND:PR:NR:PU:NU:TG:VG ./.:0:1:3:2:28:19:28:19:3:2:3:2 ./.:2:2:9:4:51:48:51:48:9:4:6:5 B 1 15903 5ba2b202-2078-11e5-a9d9-adff273a0828 G GC 207 F012;F010;F015 PC=I;RS=15903;RE=15906;LEN=1;S1=32;S2=838.836;REP=1;F017 GT:PP:NP:PB:NB:PD:ND:PR:NR:PU:NU:TG:VG ./.:2:0:4:0:12:2:12:2:4:0:3:2 ./.:13:1:22:1:39:19:39:19:22:1:6:7
Thank you for your help,