gymreklab/strdenovotools

Toolkit for calling and analyzing de novo STR mutations

strdenovotools's Issues

Error while running MonSTR

Hello,

I'm running MonsTR with the following options:

MonSTR \ --strvcf Family_681_209.gangSTR_filtered.CR80.vcf.gz \ --fam families.fam \ --max-num-alleles 100 \ --include-invariant \ --gangstr \ --require-all-children \ --output-all-loci \ --min-num-encl-child 1 \ --max-perc-encl-parent 0.05 \ --min-encl-match 0.9 \ --min-total-encl 10 \ --posterior-threshold 0.5 \ --default-prior -3 \ --out Family_681_209.MonSTR_analysis

and I get this error:

[MonSTR-2.0] ERROR: Required INFO field GRID not present in VCF

I noticed that the gangSTR-generated VCFs do indeed have the GRID field in the INFO column, but when I do the merge with mergeSTR they are not longer included, so mergeSTR removes the GRID info column. This is the mergeSTR command I used to merge the files.

mergeSTR \ --vcfs sample1.vcf.gz,sample2.vcf.gz,sample3.vcf.gz,sample4.vcf.gz,sample5.vcf.gz,sample6.vcf.gz \ --out Family_681_209.gangSTR_filtered \ --vcftype gangstr

Is this a mistake done mergeSTR? I'm using version 4.2.1
MonSTR only works if I use the option --naive, but I know that this are not the optimal results because they are not considering the likelihoods.

I'll appreciate your help.

B.

ERROR: Failed to extract string FORMAT value from VCF record

I ran into this error when running monSTR on VCFs created by gangSTR. I was able to trace back the error--MonSTR was looking for a field called ENCLREADS in the VCF file, and the version of GangSTR I used didn't output this field. I was using GangSTR v. 2.4 that's included in the docker image gymreklab/str-toolkit (https://hub.docker.com/r/gymreklab/str-toolkit). Switching over to GangSTR v. 2.5 fixed the problem.

I didn't see anything about this in the Github README page and the error message was vague enough that I thought I should post an issue.

Anastasia

GangSTR Command

singularity exec durga_cache/str-toolkit.simg  \
	GangSTR \
		--bam $bamfiles \
		--ref $fasta \
		--regions hg19_ver13_1.bed \
		--out $tmp_dir/$family \
		--include-ggl 

MonSTR command

MonSTR \
     --strvcf $vcf \
     --fam $ped \
     --gangstr \
     --out $out \
     --region chr19 

Error message

[MonSTR-2.0] ProgressMeter: PedigreeSet has 1 nuclear families with STR data.
Unaffected children: 2
Affected children: 0
Unknown children: 0
[MonSTR-2.0] ProgressMeter: Running de novo analysis...
[MonSTR-2.0] ProgressMeter: Opening priors file...
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:64420-64429 with 5 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:68062-68073 with 8 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:73165-73179 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:77098-77113 with 7 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:81518-81529 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:82229-82240 with 7 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:84718-84729 with 5 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:86447-86478 with 7 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:88826-88837 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:92094-92119 with 12 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:92177-92191 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:98941-98952 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:111045-111059 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:121729-121738 with 5 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:124645-124656 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:127790-127801 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:128904-128915 with 9 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:141013-141027 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:141556-141567 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:161680-161691 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:164287-164302 with 7 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:178430-178439 with 5 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:183794-183805 with 7 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:184457-184468 with 6 alleles.
[MonSTR-2.0] ProgressMeter: Processing STR region chr19:185253-185264 with 8 alleles.
[MonSTR-2.0] ERROR: Failed to extract string FORMAT value from VCF record