Gymrek Lab comments

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                                            Gymrek Lab

Problem with read IDs repeated in the same BAM file

Using HipSTR version v.0.6.1 ``` ./HipSTR/HipSTR --version HipSTR version v0.6.1 ``` Attached files for the command below [chr9.testregions.bed.zip](https://github.com/tfwillems/HipSTR/files/1672249/chr9.testregions.bed.zip) [hipstr_error_reads.bam.zip](https://github.com/tfwillems/HipSTR/files/1672237/hipstr_error_reads.bam.zip) Command: ``` HipSTR \ --bams hipstr_error_reads.bam \ --fasta /storage/resources/dbase/human/GRCh38/GRCh38_full_analysis_set_plus_decoy_hla.fa \ --regions...

script lobSTR_filter_vcf.py failure

Thanks for the comment. When you say fail, do you mean the script crashes, or that the output is not as expected? Lines 175-178 were intended to deal with this...

We need testing around ploidy

HipSTR has an option `--haploid-chrs` to specify a chromosome as haploid. ExpansionHunter has an `--sex` option which I assume is used for ploidy of sex chromosomes. Agree we should add...

Feature Request: Rasterize PDFs

That would be great! Another option could be to have savefig save them as .png or another format.