I want to filter my VCF file to include only the relevant information I need but I have some questions about the results I got.
This is what the first 10 lines of my VCF file looks like:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DATA_VARIANT chrI 826 . T C 255 . CNV=1 GT:PL:GQ:DP:BSDP:ACN 1/1:344,30,0:57:10:0,10,0,0:0,5 chrI 831 . C T 71 . CNV=1 GT:PL:GQ:DP:BSDP:ACN 0/1:139,36,274:71:12:0,8,0,4:3,2 chrI 836 . G T 59 . CNV=1 GT:PL:GQ:DP:BSDP:ACN 0/1:140,49,373:59:16:0,0,12,4:4,1 chrI 848 . C T 255 . CNV=1 GT:PL:GQ:DP:BSDP:ACN 1/1:556,48,0:75:16:0,0,0,16:0,5 chrI 855 . G A 255 . CNV=1 GT:PL:GQ:DP:BSDP:ACN 0/1:399,48,139:59:16:12,0,4,0:1,4 chrI 858 . ATT AT 255 . CNV=1;TYPE=INDEL GT:PL:GQ:DP:ADP:ACN 0/1:480,48,160:85:16:4,12:1,4 chrI 876 . T C 255 . CNV=1 GT:PL:GQ:DP:BSDP:ACN 1/1:865,75,0:102:25:0,25,0,0:0,5 chrI 904 . G A 255 . CNV=1 GT:PL:GQ:DP:BSDP:ACN 1/1:1261,112,0:138:37:37,0,0,0:0,5 chrI 920 . A T 67 . CNV=1 GT:PL:GQ:DP:BSDP:ACN 0/1:244,145,1426:67:48:41,0,0,7:4,1 chrI 925 . T C 255 . CNV=1 GT:PL:GQ:DP:BSDP:ACN 1/1:1786,157,1:255:52:0,52,0,0:0,5
QUAL: As I understand it, the QUAL is based off of Phred quality scores, which would mean that a QUAL value of anything greater than 20 would be fairly sufficient in terms of quality for that genotype. However, most of my QUAL scores are 255 and from what I've read that means there is no mapping quality available?
- What does this mean for my data? I used the same tool (NGSEP) to map and call the variants on this strain so it should have mapping quality scores.
- Do I need to filter out all the 255 scores? Or can they still be used?
PL: From what I've read about PL scores, they indicate the likelihood of the presence of a genotype (0/0, 0/1, 1/1). Based on the results, there should be a clear least likely genotype, "almost" likely genotype, and a most likely genotype indicated by a value of 0.
- Some of my PL values do not include a 0 (i.e., the second variant call = 139,36,274). What does this mean for my data?
Any help would be great! Thank you!
Note: I used NGSEP as my variant caller