Error with "read_vcfs_as_granges" function

[shaghayeghsoudi]

Dear developers,

I am trying to run MutaionalPattern and my original data are in MAF file format, however as the tool requires vcf file format I converted my maf files into vcf files.

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRC125_postRT
1	168266966	1:168266966_C/T	C	T	.	.	t_alt_count=6;t_ref_count=49	AD:DP	.,6:49
2	196922779	2:196922779_A/T	A	T	.	.	t_alt_count=30;t_ref_count=74	AD:DP	.,30:74
1	114267511	1:114267511_A/C	A	C	.	.	t_alt_count=40;t_ref_count=15	AD:DP	.,40:15

Unfortunately I cannot get the tool running and keep getting this warning message

[E::COMPAT_vcf_hdr_read] No sample line
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'granges': error in evaluating the argument 'x' in selecting a method for function 'seqinfo': no 'header' line "#CHROM POS ID..."?

I have not idea because the header line is present.
Can you please provide me with some advice how to solve this problem?
Thank you

[rhagelaar]

Dear Shaghayegh,

When I take your input and try to run the following command :
grl.maf <- read_vcfs_as_granges(vcf_files = "maf_input.vcf", sample_names = "MAF_format", ref_genome)

I get a slightly different error

[E::COMPAT_bcf_hdr_read] Input is not detected as bcf or vcf format
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'granges': error in evaluating the argument 'x' in selecting a method for function 'seqinfo': no 'header' line "#CHROM POS ID..."?

This suggest that the input is not in VCF format. If I add the following header(s) to your example file it accepts the file and returns a grangeslist

##fileformat=VCFv4.2
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">

Some background information. VCF format requires a header for each type of in your format column. So if you have more, these need to be added as wel.

Hope this helps