How we can put PASS filters on all variants in your VCF file and create a separate file?

Question

[astrava]

By default, we trust PASS filters on VCF files. If a VCF is not filtered or PASS filters are not present, we use a very basic universal filter that relies on QUAL (Quality) and DP (Depth), which is better than nothing. If you want to run all of your data through GenVue Discovery regardless of quality, you or your provider must put PASS filters on all variants in your VCF file. I have us.dantelabs.com file hg19 /GRCh37

**291.raw.vcf** 
##fileformat=VCFv4.2

##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample">


#contig=<ID=hs37d5,length=35477943>
##reference=file:///references/grch37/reference.bin
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  291
1   10177   .   A   AC  43.52   .   AC=1;AF=0.500;AN=2;DP=114;FS=13.306;MQ=25.21;MQRankSum=-2.232;QD=0.38;ReadPosRankSum=1.146;SOR=0.617;FractionInformativeReads=0.658;R2_5P_bias=-17.815  GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB    0/1:15,60:0.800:75:3,32:12,28:6:44,0,1:4.3520e+01,1.3955e+00,5.6103e+00:0.00,2.00,5.00:11,4,26,34:7,8,28,32
1   10230   .   AC  A   42.13   .   AC=1;AF=0.500;AN=2;DP=122;FS=10.543;MQ=25.94;MQRankSum=-1.250;QD=0.35;ReadPosRankSum=1.088;SOR=1.888;FractionInformativeReads=0.672;R2_5P_bias=4.813    GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB    0/1:32,50:0.610:82:18,24:14,26:37:72,0,35:4.2129e+01,9.0222e-04,3.8342e+01:0.00,30.00,33.00:14,18,12,38:16,16,28,22
1   10247   .   TA  T   28.14   .   AC=1;AF=0.500;AN=2;DP=110;FS=2.032;MQ=27.83;MQRankSum=0.279;QD=0.26;ReadPosRankSum=1.158;SOR=1.042;FractionInformativeReads=0.709;R2_5P_bias=6.131  GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB    0/1:49,29:0.372:78:26,14:23,15:28:63,0,46:2.8143e+01,6.7236e-03,4.8757e+01:0.00,35.00,38.00:19,30,9,20:28,21,12,17
1   10254   .   TA  T   42.11   .   AC=1;AF=0.500;AN=2;DP=110;FS=4.298;MQ=27.96;MQRankSum=-0.433;QD=0.38;ReadPosRankSum=1.726;SOR=1.207;FractionInformativeReads=0.755;R2_5P_bias=-18.055   GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB    0/1:41,42:0.506:83:23,18:18,24:41:77,0,46:4.2107e+01,3.2540e-04,4.8750e+01:0.00,35.00,38.00:18,23,14,28:22,19,20,22
1   10285   .   T   C   33.09   .   AC=1;AF=0.500;AN=2;DP=132;FS=5.110;MQ=22.46;MQRankSum=1.791;QD=0.25;ReadPosRankSum=3.403;SOR=1.415;FractionInformativeReads=0.545;R2_5P_bias=-9.574 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB    

[brunobsouzaa]

Use GATK VariantFiltration and set the filters and thresholds for each filter. The ones that met all criteria, will be set as PASS.

[astrava]

Thanks, I'm reading https://gatk.broadinstitute.org/hc/en-us/articles/360037434691-VariantFiltration

Answer 1

[astrava]

Inputs

A VCF of variant calls to filter.
One or more filtering expressions and corresponding filter names.

Output

A filtered VCF in which passing variants are annotated as PASS and failing variants are annotated with the name(s) of the filter(s) they failed. Usage example

 gatk VariantFiltration \
   -R reference.fasta \
   -V input.vcf.gz \
   -O output.vcf.gz \
   --filterExpression "AB < 0.2 || MQ0 > 50" \
   --filterName "my_filters"

Answer 2

[astrava]

PF for pass-filter. illumina sequencers perform an internal quality filtering procedure called chastity filter, and reads that pass this filter are called PF for pass-filter. According to Illumina, chastity is defined as the ratio of the brightest base intensity divided by the sum of the brightest and second brightest base intensities. Clusters of reads pass the filter if no more than 1 base call has a chastity value below 0.6 in the first 25 cycles. This filtration process removes the least reliable clusters from the image analysis results.