Closed cboustred closed 9 years ago
bcftools isec platypus_chr22_normal_filt.vcf.gz freebayes_chr22_normal_filt.vcf.gz -p dir
Also works as expected reporting ~561 shared variants using the freebayes vcf
The contigs in the headers of the vcf files have to be the same for vt partition to work. Are the headers the same?
Bingo, that did the trick! Thanks very much! Chris
Thanks for reporting this, I'll add a check for that later.
fixed.
Hi,
I'd like to use vt partition to identify the similarities and differences between variants called by different variant callers on the same set of samples.
However I'm having some issues...
partition v0.5 Options: input VCF file a platypus_chr22_normal_filt.vcf.gz input VCF file b freebayes_chr22_normal_filt.vcf.gz A: 663 variants B: 609 variants ts/tv ins/del A-B 663 [3.04] [1.20] A&B 0 [-nan] [-nan] B-A 609 [3.12] [1.50] of A 0.0% of B 0.0% Time elapsed: 0.02s
i.e. there are zero overlaps between variants in the two files
However, using vcftools I can see there are ~565 variant overlaps between variants in the two files:
vcf-isec -f platypus_chr22_normal_filt.vcf.gz freebayes_chr22_normal_filt.vcf.gz | grep -v ^# | wc -l 565
Any thoughts as to why vt partition would not be working? It appears to be an issue with the Freebayes VCF as when I do a comparison with a VCF generated with VarScan2 I get results as expected from vt parition:
vt partition varscan_chr22_normal.vcf platypus_chr22_normal_filt.vcf.gz
partition v0.5 Options: input VCF file a varscan_chr22_normal.vcf input VCF file b platypus_chr22_normal_filt.vcf.gz A: 673 variants B: 663 variants ts/tv ins/del A-B 97 [2.36] [1.00] A&B 576 [2.93] [1.50] B-A 87 [3.73] [0.75] of A 85.6% of B 86.9% Time elapsed: 0.02s
Using vt partition + varscan vcf + freebayes vcf returns 0 overlap hence why I think it is an issue with the freebayes VCF.
I have run vt partition comparing the freebayes vcf to itself and that returns as expected results: vt partition freebayes_chr22_normal_filt.vcf.gz freebayes_chr22_normal_filt.vcf.gz partition v0.5
Options: input VCF file a freebayes_chr22_normal_filt.vcf.gz input VCF file b freebayes_chr22_normal_filt.vcf.gz A: 609 variants B: 609 variants ts/tv ins/del A-B 0 [-nan] [-nan] A&B 609 [3.12] [1.50] B-A 0 [-nan] [-nan] of A 100.0% of B 100.0% Time elapsed: 0.03s
Commands for generating the Freebayes VCF were this:
Any help with this much appreciated
BW
Chris