Zamin Iqbal

Output contigs in GFA format?

2

Any plans to output your actual contigs in GFA?

vcfcombine takes files with many sites and produces a tiny file

17

I've got 2 VCF files with 671,775 PASS lines in each. Both VCFs have the same 1st 9 columns - just the sample columns differ When I try this vcflib/bin/vcfcombine...

Performance cost of kmer-indexing

1

This is perhaps an interesting datum. Building the PRG (by which i mean "gramtools build") for 1.3kb of the TB genome, combining calls from 50,000 TB, we find there the...

The human genome is 3billion bases and the MHC is 5Mb long. This PRG just contains the 8 reference MHC haplotypes, but no other variation - so 99.8% of the...

Systematic decisions to ignore regions of the PRG

8

Given a (minimum and) maximum read length, and a PRG,we should be able to 1. decide that there are some places we will never be able to draw inference on,...

What to do with smaller genomes?

8

Hi there Congratulations on a very nicely written paper. I'm still absorbing it, but I wondered what I ought to do if using it on small genomes. Your documentation says...

This is because of this line https://github.com/iqbal-lab/cortex/blob/6d8e2f9f1984651c253bdd9d748acf6efa54c165/scripts/calling/run_calls.pl#L1511 one solution might be to simply print VCF header here

Just got this error message running run_calls in the clockwork singularity container. ``` Possible precedence issue with control flow operator at /bioinf-tools/cortex/scripts/analyse_variants/bioinf-perl/lib/RefGenome.pm line 287. Possible precedence issue with control flow...

Fix known bugs in genotyping and look at confidence distribution

6

To fix: 1. poisson error rate uses estimates of total read count - prefer to use median depth 2. improve gt confidence

Improve mem height/width estimation in run_indep_workflow...

4

..as Rachel says it consistently underestimates mem required.