Errors when running COBALT and AMBER with v37 test data

[bobrad98]

Hi,

I tried running the latest versions of AMBER and COBALT with the test alignment and HMFTools-Resources > DNA-Resources (v37) data that you provided, but both of them failed.

AMBER returned the following error:

Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /HMFtools-Resources_dna_pipeline_v5_31_37_copy_number_GermlineHetPon.37.vcf

which suggests that the VCF file isn't formatted as it should be.

Error log in COBALT contained the following error:

ERROR 2023-01-23 17:19:24 ValidateSamFile Cannot use index file with textual SAM file

I tried to check both BAM files with Picard's ValidateSamFile. The tumor file returned with no errors, but the tool wouldn't work for the reference file with the same error that COBALT returned.

Can you please check these files?

[bobrad98]

Update:

Using bcftools view with your VCF file as input, I managed to create a valid VCF file. Unfortunately, AMBER still doesn't work - and it prints the same error message as COBALT

[hongwingl]

Hi, I tried running ValidateSamFile with those bams, it seems to be fine. Have you tried redownloading the reference bam file again?

[bobrad98]

Hi,

Yes, I tried redownloading it multiple times. I'll try it again, maybe I clicked something wrong

[bobrad98]

Yes, it is valid - I probably didn't download it properly. Thanks!