bergeycm / ngs-map Goto Github PK

I am attempting to convert a VCF tabular file into a FASTA alignment.
Here is the command line I use when attempting to do this:
perl vcf_tab_to_fasta_alignment.pl -i snps.tab > snps.tab.fasta
Here is what the data snps.tab looks like:
#CHROM POS REF T44 T46 T51 T60 T73 T88
1 214304 G G/A G/A G/A G/G G/G G/G
1 381695 C T/T C/T C/C C/C C/C C/C
1 830338 C C/G C/G C/G ./. C/C C/C
1 868662 G G/G G/G G/G G/A G/G G/A
1 1282509 A A/C A/A A/C A/A A/A A/A
1 2180028 T T/T T/T T/T T/T T/C T/C
1 3774988 A A/A A/A A/A A/A A/G A/G
1 3920742 A A/A A/G A/A A/G A/G G/G
1 4776967 G G/G G/T G/T T/T T/T G/T
1 5014432 C C/C C/C C/C C/T C/T C/C
1 5344204 G G/G G/G G/G G/G G/T G/T
However, I continually get this error(ERROR: Could not open input file -i.)
I really don't kown how to solve it !I will really appreciate if someone can help out.

Hi Christina,

I think since you published this script 2012 time, it has travelled quite a bit ... I found it copied into a copy of vcftools lying around our lab in Scotland here.

What happens in these occasions is that small ad-hoc edits are made, sometimes in a rush, and the output may be different to what you as author intended. For such situations, and dspite it being a small script as you call it, it could benefit from more inline documentation so that people will edit more wisely, and less in a rush.

So this isn't a bug or an issue as such, rather a heads-up that your script is actually pretty famous, and it may be an idea to look at the old version posted on google code and to include a link to the latest version (which I assume is in this repository) and to advise users to update.

I'll fork it and include my own notes for good measure.

Cheers / Ramon.

Additional file with all sites (not just variants) should be output. Run separately with --output_mode set to EMIT_ALL_CONFIDENT_SITES in GATK UnifiedGenotyper. Change PBS scripts too. See documentation. This is for downstream analyses like calculating nucleotide diversity.