jjfarrell

I am also interested in this feature for genotyping across a cohort of 5k samples.

@dglazer The core concept described earlier does capture the data flow found in joint genotyping to create a multi-sample analysis ready VCF (as found in the GATK pipeline https://www.broadinstitute.org/gatk/guide/bp_step.php?p=2). In...

There are two situations for unmapped reads for paired-ends. 1. One Paired-End is mapped and the other is not. The unmapped is given the mapped end position but marked as...

On this run, we got a segfault memory error. Working with 52877 samples Identifying relatives for each sample using kinship threshold 0.0220970869120796 Identifying pairs of divergent samples using divergence threshold...

We are running with 196GB of memory with 28  cores.  What is a recommended amount of memory per core be?  

We were able to run the PCs on 45k unrelated and then project it on the remaining 8k samples successfully.

@jonassibbesen I have found the one variant that is triggering this error and created a vcf that I can share. let me know how to get it to you.

@lprada and @jonassibbesen I eventually found the source of the error. I typically use bgzip to compress vcf files. That allows the file to be indexed. For the candidate vcf...

Here is one approach I think might work-At the insertion sites, the cigar should have an "I" in the read. So the depth of the insertion would be the number...

I tried it both ways (all N and all T) for just those 4 variants and it worked fine. If I make the variants with a mix of 3 Ts...