MN908947.3 694 . T A 54.15 PASS DP=2813;AC=40,25;AM=2748;MC=0;MF=0.0;MB=0.0;AQ=4.55;GM=1;PH=6.02,6.02,6.02,6.02;SC=None; GT:GQ:PS:UG:UQ 0/1:54.15:.:0/1:54.15
And the pass.vcf I have:
MN908947.3 685 . AAAGTCATTT A 500.0 PASS DP=2812;AC=2,2810;AM=0;MC=0;MF=0.0;MB=0.0;AQ=35.89;GM=1;PH=6.02,6.02,6.02,6.02;SC=None; GT:GQ:PS:UG:UQ 1/1:500.0:.:1/1:500.0
MN908947.3 691 . AT A 500.0 PASS DP=2813;AC=0,2489;AM=324;MC=0;MF=0.0;MB=0.0;AQ=10.48;GM=1;PH=6.02,6.02,6.02,6.02;SC=None; GT:GQ:PS:UG:UQ 1/1:500.0:.:1/1:500.0
When artic_mask is run, AAAGTCATTT becomes AAAGTCATTN in the preconsensus.fasta, and as a consequence bcftools complains:
Note: the --sample option not given, applying all records regardless of the genotype
The fasta sequence does not match the REF allele at MN908947.3:685:
REF .vcf: [AAAGTCATTT]
ALT .vcf: [A]
REF .fa : [AAAGTCATTN]GACTTAG.....
What would be your recommended procedure in these very rare cases? Ignore the fail.vcf, mask the variant in the pass.vcf?
Hello!
This is somewhat related to https://github.com/artic-network/fieldbioinformatics/issues/53
In my
fail.vcf
I have:And the
pass.vcf
I have:When
artic_mask
is run,AAAGTCATTT
becomesAAAGTCATTN
in thepreconsensus.fasta
, and as a consequencebcftools
complains:What would be your recommended procedure in these very rare cases? Ignore the
fail.vcf
, mask the variant in thepass.vcf
?