unified genotyper targetfile

Question

[datanerd]

HI all,

I have a quick question if someone can help.

I am trying to use UnifiedGenotypper for variant calling, however no matter what file I use for -L target interval (I downloaded from Illumina websites, UCSC) but it gives me error

File associated with name gr37Exons.bed is malformed: Problem reading the interval file caused by Badly formed genome loc: Contig chr1 given as location, but this contig isn't present in the Fasta sequence dictionary

Can someone help me with this??

Thanks in advance

Mamta

[datanerd]

Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:

##### ERROR   contig reads = 10 / 135524748
##### ERROR   contig reference = 10 / 135534747

This is what I get now. I had used b37 for alignment and same is the ref file.

Answer 1

[Ram]

Maybe your reference sequence has different naming conventions for the chromosomes (1 instead of the expected chr1) - might wanna check that.

If so, change your intervals file to match the naming convention from the ref file

[datanerd]

Thanks, I tried that. But now I get a different error

Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:

Any help?