segfault at basic qc step about mocha HOT 6 CLOSED

It will not have a huge impact, but you could run MoChA on the unphased VCF and it will generate a summary file with the sex column which you could use to complete the QC before you phase the data. I will include this information in the next update.

from mocha.

I have just tried to run your command using my own version of dup.grch37.bed.gz/dup.grch37.bed.gz.tbi and it works for me. This is what that file should contain:

$ zcat dup.grch37.bed.gz | head
1	10000	10485	0.00713299
1	10485	18392	0.00579252
1	18392	87112	0.00457824
1	87113	88000	0.00686326
1	88000	110582	0.00653207
1	110582	139463	0.00485026
1	139463	154500	0.00317143
1	154500	173929	0.00214293
1	173929	177417	0.00201696
1	227417	228316	0.011709

In any case, I did not write bcftools annotate. Make sure you use one of the latest versions of bcftools (e.g. 1.9-83-gb406a39) and, if you can reproduce the error, then maybe file a bug report with the maintainer of bcftools.

from mocha.

Somehow I'm missing the 4th column in my dup file. I suppose that's why I'm getting the segfault.
Edit: Need to remove the cut command as mentioned in issue #2

from mocha.

My bad indeed. I fixed the README. Thank you for reporting the issue now. Still, bcftools annotate should have given you a proper error message rather than segfault.

from mocha.

On a separate note, I don't know my sample's gender so I generated the exclusion list without the sex test. Will it have significant impact on the phasing and mocha results?

from mocha.

My bad indeed. I fixed the README. Thank you for reporting the issue now. Still, bcftools annotate should have given you a proper error message rather than segfault.

Thank you for your prompt reply and help!

from mocha.