Ismail Moghul

Hey, Firstly thank you for this library - It has been amazing so far :). I would also like to do this - i.e. capture the input value and use...

This looks amazing! Thank you very much for taking the time to implement this 👍

have updated above msg with other suggestions/issues wrt error reporting

Further to above, the `gemBS call` has finished and I have the following errors, Any idea what is causing them? I've rerun the samples (i.e. remove associated files and a...

The above errors disappeared when repeatedly deleting the relevant files and rerunning. Moreover, the two samples that failed were of a much higher coverage (i.e. greater than 90X) than the...

That was the first thing I checked - there was a few TB of free space.

No, but it doesn't exist in the query BAM file either: ``` $ samtools view -H EGAZ00001016574_90.bam | grep chr14_GL @SQ SN:chr14_GL000009v2_random LN:201709 @SQ SN:chr14_GL000225v1_random LN:211173 @SQ SN:chr14_GL000194v1_random LN:191469 ```

Yes they do ``` $ zcat hg38.fa.gz| grep chr14_GL >chr14_GL000009v2_random >chr14_GL000225v1_random >chr14_GL000194v1_random ```

I understand. As mentioned above, I managed to 'fix' the problems by simply rerunning the analysis repeatedly. If I do see something similar again, I will raise an issue here....

Hi, I managed to fix the above gemBS index error by extracting chromosomes 1-22 XY from the VCF (it seems that it was the PATCH chromosomes in the dbsnp vcf...