Zamin Iqbal

Results 180 comments of Zamin Iqbal

Output contigs in GFA format?

Use-case = that GFA represents your final assembly graph. You take your links+DBG and infer contigs, plus at the end of each contig you have edges, and the string graph...

2-color cortex?

And to follow up @yannickwurm - Mccortex already does this (not sure if I was clear) - it allows longer range paths to be stored. What it does not have...

Is it possible to extract kmers in bubbles?

for the first question @noporpoise will know. It's not much help, but cortex can consume mccortex binary graphs, and i know cortex bubble calling does output exactly what you want...

Is it possible to extract kmers in bubbles?

Dammit I need to close the source forge page. Sorry. Current page is https://github.com/iqbal-lab/cortex

vcfcombine takes files with many sites and produces a tiny file

Ah. I bet it is because vcfcombine dies if there are overlapping records

vcfcombine takes files with many sites and produces a tiny file

It's my fault (yes, I can share if you like) - i have a lot of lines in these VCFs which overlap. I just wanted to ignore that, and "cat...

vcfcombine takes files with many sites and produces a tiny file

So what would you do with chr1 1 A G chr1 10 AAAAAA AAGATAGAGAA chr1 11 AAA TTAT chr1 13 AAA GGAGA leave aside the issue of left-alignment and the...

vcfcombine takes files with many sites and produces a tiny file

For all my VCFs, the first 9 columns are 100% identical. It's only the genotyping column that differs. So that ought to work...

vcfcombine takes files with many sites and produces a tiny file

OK, there is still an issue. I have 2 files, with totally identical isolated SNPs within them -bash-4.1$ grep -c PASS file1.vcf 26892 -bash-4.1$ grep -c PASS file2.vcf 26892 vcflib/bin/vcfcombine...

vcfcombine takes files with many sites and produces a tiny file

Any way I can attach VCFs to this?