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"Stéphane Plaisance" <Stephane....@vib.be>: Apr 18 11:46AM
Hi Len and all,
Ref: https://www.biostars.org/p/182127/
Can you please give a bit more help on how to adapt a dbSNP.vcf file to be used in vcfeval as -b input
Do we have to engineer a 9th FORMAT column with GT and a 10th column ‘ALT’ as sample name and 1 as content for the whole file?
Like this awk does:
```
awk 'BEGIN{FS="\t"; OFS="\t"}{if ($0~/^##/) print $0; else if($0~/#CHROM/) print $0,"FORMAT","ALT"; else print $0,"GT",1}' gallus_gallus.vcf | bgzip -c > gallus_gallus_alt.vcf.gz.vcf
```
Thanks in advance,
Stephane
PS my chicken database looks like this:
#CHROM POS ID REF ALT QUAL FILTER INFO
1 249857 rs735818313 C A . . E_Multiple_observations;TSA=SNV;dbSNP_150
1 289870 rs1060254042 T C . . TSA=SNV;dbSNP_150
1 318447 rs1060384925 C A . . TSA=SNV;dbSNP_150
1 394741 rs16728075 G A . . E_Freq;TSA=SNV;dbSNP_150
1 394744 rs16728074 G A . . E_Freq;TSA=SNV;dbSNP_150
1 394746 rs16728073 C T . . E_Freq;TSA=SNV;dbSNP_150
1 394765 rs741618862 T A . . TSA=SNV;dbSNP_150
1 394776 rs731376058 T C . . TSA=SNV;dbSNP_150
…
--
Stephane Plaisance – NGS analysis specialist
VIB Nucleomics Core
Herestraat 49 – Post Box 816 – 3000 Leuven – Belgium
O&N4 Building – 8th Floor – Room 08.429
Tel. +32 16 32 00 60
www.nucleomicscore.sites.vib.be<https://nucleomicscore.sites.vib.be/en>
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Len Trigg <l...@realtimegenomics.com>: Apr 19 08:29AM +1200
Hi Stéphane,
Hope all is well with you. You should be able to use the dbSNP VCF file
directly without having to alter it. The trick though is that you need to
use the --sample flag to tell it to work directly from the ALT alleles in
the baseline file (-b). You will want either --sample ALT,ALT (for the case
where your calls (-c) file also has no sample column), or --sample
ALT,mysample (for the case where your calls has a sample column named
"mysample"). You probably also want --squash-ploidy when using such
database files.
Cheers,
Len.
On Tue, 18 Apr 2023 at 23:46, Stéphane Plaisance <Stephane....@vib.be>
wrote:
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