Nils Homer

A tool that can downsample a BAM many times

1

I'd like a tool that reads an input BAM to downsample only _once_, and then produces `N` downsampled BAMs, each corresponding to a different downsampling proportion. I also wonder if...

This variant is normalized (confirmed by running `vt`) but wrongly reported as not normalized when running with `--forceGT` and supplying the known VCF (in this case dbsnp). ``` chr22 16647586...

Activate conda environment

9

I frequently have docker images with one or more conda environments installed. When I run a WDL task, I need to add following to my command each time: ```wdl command

Keep going with independent tasks

5

When a WDL task fails (run via AGC), I've observed that all other tasks are killed. I'd like `miniwdl` to execute as many tasks as possible until there are no...

Clarify MI for identifying source molecule strand

14

For duplex sequencing technology, we can identify the _strand_ (top or bottom) from which the read was derived relative to the duplex source molecule. This _convention_ or _recommendation_ would allow...

VCF Header: must Number be before Type?

17

### Background We were trying to process a VCF with htsjdk from here: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/1kGP_high_coverage_Illumina.chr20.filtered.SNV_INDEL_SV_phased_panel.vcf.gz And I got the following exception: ```console Exception in thread "main" htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header...

VCF FILTER COLUMN "." value - to PASS or not to PASS, that is the question:

5

When the FILTER column in a VCF ".", is that a PASS variant or not or something else? Motivation: I was using `pysam`'s `VariantRecord` and noticed that when the VCF...

Specify "is autosomal" or provide ploidy of a sequence record

4

So many tools and groups hard-code or have lists of which contigs are autosomal, or even a specific ploidy (looking at you plant genomes). I wanted to start a discussion...

Request: Expose the minimum weighted purity filter value

1

This was available for v2.x.x and no longer for 3.x.x. I think the relevant lines are here: https://github.com/Illumina/ExpansionHunter/blob/e2a9c5bbb604abf96a3c50f1066725ef23726aa0/region_analysis/LocusAnalyzer.cpp#L190-L191

Bedtools /dev/stdin behaves differently that just stdin

3

This ```bash $cat a.bed \ | bedtools subtract -a /dev/stdin -b b.bed | bedtools subtract -a /dev/stdin -b c.bed \ > out.bed ``` yields ```text ***** WARNING: File /dev/stdin has...