seboyden

I'd like support for s.unaffected and s.unknown. Treating "affected" as a Boolean (only allowing s.affected or !s.affected) doesn't distinguish between unaffected (phenotype 1) and unknown (phenotype 0). If you don't...

csi index is now default in v0.2.7 but would be great to add an option to the Smoove command line to specify either bai or csi indices because some software...

To clarify, I did not include the HLA alt contigs in my regions file, I only included the primary contigs (chr1-chrX,chrY,chrM). The error occurred while processing chr6 (the HLA locus...

Note that the HLA alt contigs with colons in the names are specific to the Broad's GATK bundle version of the hg38 reference, they are not found in the NCBI/UCSC...

Update-- I tried re-running graphtyper providing a different reference FASTA file without HLA alt contigs. However, I got a similar error referring to a missing HLA contig in the FAI...

I've also been having memory issues trying to joint genotype the Phase3 1000 Genomes WGS data (2504 samples at 30X). On nodes with 190 Gb memory and parallelizing by chromosome,...

Thanks Hannes-- I tried v2.6.0-dev with ```--avg_cov_by_readlen``` as you described, but I still have some intervals failing on memory (2504 samples with 30X WGS, 190 Gb nodes, 64 CPUs, 3...

I finally got this to work (2504 samples with 30X WGS, 190 Gb nodes using v2.6.0-dev with ```--avg_cov_by_readlen```) by using ```--max_files_open=128``` and ```--threads=64```. Whether or not it failed on memory...

Correction-- sorry you're right they were in the svimmer output. Three examples below. It looks like graphtyper has trimmed the REF/ALT alleles, increased POS accordingly, but then set INFO/END equal...

You can just make a region file manually that lists every chromosome. Or you can pull the primary contigs out of your reference FASTA's index file, e.g.: ``` head -25...