Danny Antaki

SVTyper fails to genotype with hg38 alignments. --split_bam (-S) is deprecated

2

I am using `Version: 0.1.2` of `speedseq` and `version: v0.1.4` of `svtyper` I have 3 bam files aligned with `bwa mem` to the hg38 reference. This is my speedseq command...

`cc1plus: error: unrecognized command line option "-std=c++11"` I cannot update gcc on my server. Do you mind amending your code so I and others with older gcc versions will be...

Do you have an example of the input file needed for the script? Which species should I include for the sequence alignment. Should the input file be tab delimited? Thanks

First off, thanks for putting a lot of effort and thought into this problem. I think your solution is on the right track and is perfect for SNPs and INDELs....