graphtyper

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killed by the cgroup out-of-memory handler

1

Hi! My memory is not fully utilized, why does this problem occur? I have run it several times, and this problem persists. Moreover, the error is only on chromosome 15....

zhachengwan

Coordinates must be > 0

1

I've started a run of graphtyper 2.7.2 with a command for a chromosome of my reference: graphtyper genotype reference.fasta --sams=$BAMLIST --sams_index=$BAILIST --region=Chr5_A_fumigatus_Af293 --threads=16 --verbose --avg_cov_by_readlen=$BAMCOV --output=test [[2023-11-16 16:15:47.364] Running the...

carolinapinapaez

why SVSIZE=number+

2

Hi, why some records are "+" for example: chr1 1391725 chr1:1391725:FG N 162 PASS ABHet=0.5;ABHom=1;AC=1;AF=0.0001139;AN=8776;END=1391725;LEFT_SVINSSEQ=AAAAGTTAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAAAAATTAGCCGGGCGAGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCCAGGGGGCGGAGCCTGCAGTGAGCCGAGATTGCGCCACTGCACTCCAGCCTGGGCGACAGCGAGACTCCGTCTCAAAAAAAA;MaxAAS=9;MaxAASR=0.5;MaxAltPP=9;NHet=1;NHomAlt=0;NHomRef=4387;NUM_MERGED_SVS=1;PASS_AC=1;PASS_AN=8774;PASS_ratio=0.9998;QD=16.2;RELATED_SV_ID=209;RIGHT_SVINSSEQ=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA;RefLen=1;SVMODEL=AGGREGATED;SVTYPE=INS;SV_ID=208;SeqDepth=158115;VarType=FG GT:FT:AD:MD:DP:RA:PP:GQ:PL 0/0:PASS:54,0:1:55:55,1:0:99:0,150,255

jingydz

All BNDs have no FORMAT:FT

6

Hi, There are no FT tags in FORMAT fields for ALL BNDs. Do you have any idea why this happen? Any idea or suggestion is appreciated. Thank you, Tingting

tgong1

Not all Svimmer INS/DEL/DUP are genotyped by grapthyper as expected

2

@hannespetur A number of svimmer SVs do not get genotyped. It is primarily an issue with INS and DUP calls but some DEL calls also are skipped. INSERTIONS ``` zgrep...

jjfarrell

SV in input VCF missed in graphtyper output VCF

2

Hi, I have used manta v1.6.0 for SV discovery and svimmer to create multi-sample VCF as the input for graphtyper v2.7.5 (graphtyper genotype_sv). I found some SVs in my input...

tgong1

Using graphtyper to create a vcf we are running into a problem of the vcf is not producing calls for samples that do have variants. Double checking with IGV we...

buchanri

Hello! When I genotyped sv , I received warnings showing segment fault(core dumped), it's joint calling of only 2 samples (30X), and I also used `avg_cov_by_readlen`, `max_files_open` and threads but...

dodudoduding

Hello! When I genotyped sv , I received warnings showing segment fault(core dumped), it's joint calling of only 2 samples (30X), and I also used `avg_cov_by_readlen`, `max_files_open` and threads but...

dodudoduding

Hello, I would like to genotype variants detected with `Mutect2`. The variants were identified from targeted sequencing of high coverage (> 500x). Do you have any parameters to recommend for...

mkyriak