Dario Strbenac

I have whole genome sequencing and some FASTQ files consist of multiple runs, each done in a different lane and flow cell. It would be desirable if the software could...

I noticed that `--split_by_lines` sometimes skips segments. Notice that segment 9 is missing in the example below. ``` $ ls Fastq_split/*SP19_008632BD_HLKNYDSXY_AGCCTCAT-TCTCTACT_L003*R1* Fastq_split/1.SP19_008632BD_HLKNYDSXY_AGCCTCAT-TCTCTACT_L003_R1.fastq.gz Fastq_split/4.SP19_008632BD_HLKNYDSXY_AGCCTCAT-TCTCTACT_L003_R1.fastq.gz Fastq_split/10.SP19_008632BD_HLKNYDSXY_AGCCTCAT-TCTCTACT_L003_R1.fastq.gz Fastq_split/5.SP19_008632BD_HLKNYDSXY_AGCCTCAT-TCTCTACT_L003_R1.fastq.gz Fastq_split/11.SP19_008632BD_HLKNYDSXY_AGCCTCAT-TCTCTACT_L003_R1.fastq.gz Fastq_split/6.SP19_008632BD_HLKNYDSXY_AGCCTCAT-TCTCTACT_L003_R1.fastq.gz Fastq_split/12.SP19_008632BD_HLKNYDSXY_AGCCTCAT-TCTCTACT_L003_R1.fastq.gz Fastq_split/7.SP19_008632BD_HLKNYDSXY_AGCCTCAT-TCTCTACT_L003_R1.fastq.gz Fastq_split/2.SP19_008632BD_HLKNYDSXY_AGCCTCAT-TCTCTACT_L003_R1.fastq.gz...

List of Chromosomes

2

Could `--chrom` accept a comma separated list of values, like `--read-groups` already does?

Describe Handling of Alternate Contigs in User Guide

1

I like to see a section in the user guide how alignments to hg38 and alternate contigs are handled. We have used bwakit's version of the reference genome with alternates,...

Provide output_folding YAML Setting

1

Similar to the currently possible `code_folding: hide`, it would be convenient to have `output_folding: hide` be a possible setting. The use case is the creation of a tutorial sheet, but...

Margin Specification Between Barchart and Set Intersection Panel

1

When the vertical size of the plotting area is reduced, the elements of the plot can overlap and mask one another. Notice in the example below how the bottom of...

I am doing somatic variant calling for whole genome sequencing. This tool could be improved to have reasonable RAM demands. ``` #PBS -l walltime=05:00:00,ncpus=26,mem=750GB #PBS -q hugemem ``` Fails after...

Incorrect AD values for Low VAF Samples

1

I have three cell lines which all have the same deletion. I followed the HaplotypeCaller-CombineVCFs-GenotypeVCFs process. However, the final AD is incorrect for the two with low VAF. You can...

postalt.js MAPQ 0 on both chr17 and Alternate Contigs

1

I have been examining some strange copy number results for the gene KANSL, which is on chr17, chr17_KI270908v1_alt and chr17_GL000258v2_alt. It turns out that almost all of the reads mapping...

I haven't seen any software that calculates average WGS coverage correctly when there are alternate contigs and decoys in the reference set (e.g. hs38DH). Perhaps bwakit should provide such a...