seboyden

Variant INFO/END position is before POS

3

Graphtyper can create variants where the END position is lower than POS. This results in a warning from bcftools concat: ``` Concatenating ./chr10/010000001-011000000.vcf.gz[W::vcf_parse] INFO/END=9321046 is smaller than POS at chr10:9321047...

Fatal error "FAI index has no entry" for GRCh38 HLA alt contig

6

Running graphtyper on GRCh38 with alt contigs, I get the following fatal error on chr6: ``` [constructor.cpp:159] FAI index has no entry for contig/chromosome 'HLA-DRB1*13' ``` Both the FASTA file...

Option to mark only optical duplicates

2

Is there a way for ```samtools markdup``` to ONLY mark optical duplicates, equivalent to Picard's ```TAGGING_POLICY=OpticalOnly``` ? This would be useful for PCR-free data, which is standard for most WGS.

Capture Coverage stats are mis-calculated when using a non-flattened target BED file

1

Running alignstats v0.9.1 on exome data using -t $TARGETBED, I saw that CapCoverageBasesXPct could be >100%, which obviously shouldn't happen. It turns out my target BED file contains some overlapping...

Full diploid genotypes for 2 short alleles

1

Current behavior is to report "nan" for allele2 if it is short. It would be nice to have an estimated allele size for both allele1 and allele2, even when both...