readmanchiu

Hi @bartcharbon, Thanks for looking into Straglr. Complex patterns with interruptions is a toughie. From my experience the reads always deviate from the complex pattern specified, like I don't think...

Hi @bartcharbon, Thanks for using Straglr in your pipeline. Yes I have been planning to produce VCF output for Straglr. If you can provide me with a sample VCF output...

v1.5.0 has been released to output VCF and `--sex` has been added https://github.com/bcgsc/straglr/blob/master/docs/vcf.md

Hi @HLHsieh, The reason is `349.2` has only 1 support read, you need at least 2 to confirm the allele. Thanks for using Straglr

I haven't tried the vip pipeline - from what you wrote, you can specify the source of Straglr and you guys are using @philres fork. Straglr's only filtering is based...

VCF output has been added to v1.5.0 Some loci may be missed possibly because provided targeted motif do not match detected motif. Feel free to send me data for investigation...

Running Straglr in the the genome scan mode will only report loci that are larger than the reference, whereas running it in the genotype mode (with loci-of-interest provided) will return...

PAVFinder identifies ITD when the duplication is reported as an insertion in the CIGAR string or a split alignment from the aligner. I tested your sequence with GMAP, and unfortunately...

A different version of GMAP may be able to capture the insertion. Will take a look of your files.

Can I have the input fasta as well? thanks