Matt Velinder issues

Results 18 issues of


                                            Matt Velinder

Compound het allele segregation in multi-generational pedigree with multiple affecteds

Hey Brent, Here's the pedigree I'm working with: ``` #Kindred_ID Sample_ID Paternal_ID Maternal_ID Sex Affection_Status Project K01 UDN019315 0 0 2 1 A1247-211214-VAR-Botto-UFAGSFAA K01 UDN032463 UDN901989 UDN019315 2 2 A1247-211214-VAR-Botto-UFAGSFAA...

make-gnotate problems

`slivar_static make-gnotate *.bgz` Seems to only have processed chr10? ``` > slivar version: 0.1.11 5d6a5990fc06b52cbb1930806d03f786cf27d267 @["make-gnotate", "gnomad.genomes.v3.1.sites.chr10.vcf.bgz", "gnomad.genomes.v3.1.sites.chr11.vcf.bgz", "gnomad.genomes.v3.1.sites.chr12.vcf.bgz", "gnomad.genomes.v3.1.sites.chr13.vcf.bgz", "gnomad.genomes.v3.1.sites.chr14.vcf.bgz", "gnomad.genomes.v3.1.sites.chr15.vcf.bgz", "gnomad.genomes.v3.1.sites.chr16.vcf.bgz", "gnomad.genomes.v3.1.sites.chr17.vcf.bgz", "gnomad.genomes.v3.1.sites.chr18.vcf.bgz", "gnomad.genomes.v3.1.sites.chr19.vcf.bgz", "gnomad.genomes.v3.1.sites.chr1.vcf.bgz", "gnomad.genomes.v3.1.sites.chr20.vcf.bgz", "gnomad.genomes.v3.1.sites.chr21.vcf.bgz", "gnomad.genomes.v3.1.sites.chr22.vcf.bgz",...

Provide warning/notification if 0 is in affected_status column of ped

To let the user know slivar is treating 0 as unafffected

segregating compound het function

A js function for segregating compound het variants, to be used with `--family-expr`

Problem using the provided GFF3 annotations

I'm having trouble using the provided GFF3 annotations from https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13.draft_v1.1.gene_annotation.v4.gff3.gz Here's what I'm doing: `bcftools csq $VCF -f chm13.draft_v1.1.fasta -g chm13.draft_v1.1.gene_annotation.v4.gff3.gz -O z -o $VCF.csq.vcf.gz` And here's my ouput: ```...

Take stdin as input for -q

Be able to pipe stdin as an input for -q Ie something like: `zcat your.vcf.gz | giggle search -i $G -q /dev/stdin`

Can't run outside of directory

Can't run outside of the directory (that it was indexed in?) ``` [u0691312@puhi:rufus_1000g]$ ~/bin/giggle/bin/giggle search -i /uufs/chpc.utah.edu/common/home/u0691312/resources/reference/GTEx_sort_b/ -q 11404X2.bam.generator.V2.overlap.hashcount.fastq.bam.vcf.bed.gz -o -v ##2 223423891 223423891 2:223423891:0:24 giggle: Could not open file...

Matt Velinder