waqasuddinkhan / macaron-genmed-labex Goto Github PK

Hi,
Could you please add release tags?
Thus I am sure to download/use the correct version and not a random commit.

Thanks.
Dylan

Hi,
In which case would you recommend the validation step? It is not very clear to me, should it be applied before or after the codon realignement step? Is it something that should be done systematically in all analysis?
Thanks

MACARON seems to fail when there are two alt alleles at a single position. For example, at chr9 pos 1380000, REF is C and alt is A,T. The code fails on this line. The traceback I'm getting is:

Generating a SnpCluster Table: Done!
Traceback (most recent call last):
File "../MACARON", line 602, in
Search_CODON(INF, TMPDIR, GATK, SNPEFF, SNPEFF_HG, JAVA_OPTIONS, FIELDS, GATK4_alt)
File "../MACARON", line 271, in Search_CODON
chgz = Change_zygo(ref, alt, zyg)
File "../MACARON", line 231, in Change_zygo
print(csp[1])
IndexError: list index out of range

The demo vcf provided in the github repo doesn't throw any errors but my vcf does. I'm pretty sure this is happening because of the two ALT alleles issue.

I have attached the .vcf. It uses GChr38.99
NVC_Output.txt

I changed the name from NVC_Output.vcf to NVC_Output.txt because Github does not allow .vcf file format

Thanks for looking into this!
@waqasuddinkhan