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mehrdadbakhtiari / adVNTR

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
http://advntr.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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vcf Output-Filter is all . instead of PASS #41

Closed psychrb closed 3 years ago

psychrb commented 3 years ago

In running adVNTR I am concerned since the FILTER column for the output vcf file is all "." for the n=6,719 loci. Please advise: This should all be "PASS", instead no?? Does this mean that these calls did not PASS? The header of adVNTR output vcf file is below and input code as per program: advntr genotype -m hg19_selected_VNTRs_Illumina.db -f FILENAME.bam --of vcf -o FILE.vcf

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FILENAME

chr1 700243 . CGAGGCGGGAAGATCACTTGATATCAGGAGTCGAGGCGGGAAGATCACTTGACGTCAGGAGTT . . . END=700306;VID=156;RU=CGAGGCGGGAAGATCACTTGACATCAGGAGTT;RC=2GT:DP:SR:FR:ML 0/0:18:6:12:0.9995 chr1 777293 . AGAAATGCTTCTTTAGAAATGCTTCTTT . . . END=777321;VID=174;RU=AGAAATGCTTCTTT;RC=2 GT:DP:SR:FR:ML 0/0:32:18:14:1.0000 chr1 900683 . TTTATTTAGTTGTTTATTTATTTAGTTATTTATCTTATTTATTGAGGGG . . . END=900732;VID=239;RU=TTTATTTAGTTATTTA;RC=3 GT:DP:SR:FR:ML 0/0:28:15:13:1.0000 chr1 910475 . GAGAAAGAAAAAAGAGAGAAGAGAGAGAGGAGAAGAGAGAAAAGAAGAGAAGAGAGAAGAGAAGAGAAGGAAAGAGAGAGAGAGAATAAGAAAAGGAAGAAAGAAAAAGAAAAGATAGAA

Jong-hun-Park commented 3 years ago

Hi, "." for FILTER column means there is no filter applied. Since adVNTR doesn't automatically apply QC steps after calling genotypes, it's set to the missing value, ".".