from Deepvariant, in one gVCF I have the following
Chrom_3 7768199 . C T,<*> 6.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:7:81:55,24,0:0.296296,0:5,0,48,990,990,990
However, it doesn't seem to have been kept in the final pVCF. I suppose it comes from the ratio of AQ (computed from PL, right)?
In that case, for DeepVariant WGS, would setting
min_AQ1: 0
min_AQ2: 0
Have the effect of keeping all variants? If I understand well, the preset for Deepvariant WGS are just to filter on AQ. Therefore I tried a custom yaml
cat config_custom.yml
unifier_config:
min_AQ1: 0
min_AQ2: 0
min_GQ: 0
monoallelic_sites_for_lost_alleles: true
max_alleles_per_site: 32
genotyper_config:
required_dp: 0
revise_genotypes: true
allow_partial_data: true
more_PL: true
trim_uncalled_alleles: true
liftover_fields:
- orig_names: [MIN_DP, DP]
name: DP
description: '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">'
type: int
combi_method: min
number: basic
count: 1
ignore_non_variants: true
- orig_names: [AD]
name: AD
description: '##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">'
type: int
number: alleles
combi_method: min
default_type: zero
count: 0
- orig_names: [GQ]
name: GQ
description: '##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">'
type: int
number: basic
combi_method: min
count: 1
ignore_non_variants: true
- orig_names: [PL]
name: PL
description: '##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype Likelihoods">'
type: int
number: genotype
combi_method: missing
count: 0
ignore_non_variants: true
but then I get
./GLnexus/glnexus_cli --config config_custom.yml *.g.vcf.gz|bcftools view|bgzip -@ 8 -c > joint_noAQfilter.vcf.gz
[17095] [2020-06-11 13:18:04.730] [GLnexus] [info] glnexus_cli release v1.2.6-0-g4d057dc Thu Mar 19 09:26:57 2020
[17095] [2020-06-11 13:18:04.730] [GLnexus] [warning] jemalloc absent, which will impede performance with high thread counts. See https://github.com/dnanexus-rnd/GLnexus/wiki/Performance
[17095] [2020-06-11 13:18:04.730] [GLnexus] [info] Loading config YAML file config_custom.yml
[17095] [2020-06-11 13:18:04.730] [GLnexus] [error] Failed to load unifier/genotyper configuration: IOError: loading configuration YAML file (config_custom.yml)
Failed to read from standard input: unknown file type
Yes to all. The AQ is only about ~5 on Phred scale. It looks to me like the indentation may just be off in your YAML -- unifier_config: and genotyper_config: should be at the same indentation level
Hello,
from Deepvariant, in one gVCF I have the following
However, it doesn't seem to have been kept in the final pVCF. I suppose it comes from the ratio of AQ (computed from PL, right)?
In that case, for DeepVariant WGS, would setting
min_AQ1: 0 min_AQ2: 0
Have the effect of keeping all variants? If I understand well, the preset for Deepvariant WGS are just to filter on AQ. Therefore I tried a custom yaml
but then I get