Question: vt normalization of dbSNP VCF
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gravatar for plink_9857
2.6 years ago by
plink_985750
United States
plink_985750 wrote:

I attempted to use the VT program (http://genome.sph.umich.edu/wiki/Vt#Installation) to normalize my GRCh37 dbSNP.VCF which was annotated beforehand using bcftools.

My question is how to avoid the error below: (BTW: I know that there are options to relax this consistency check so that the error doesn't pop-up, but when I relaxed the consistency check, the vt program found differences between the entire Chromosome Y sequences (REF) and the entire Chromosome Y sequences in the GRCh37 fasta that has an additional contig section in its header).

Any suggestions?

The error message:

[variant_manip.cpp:96 is_not_ref_consistent] reference bases not consistent: Y:10019-10019 T(REF) vs N(FASTA)

Here is my command for the VT program:

margaret@SII-T7500-01:~/Programs/vt$ ./vt sort -m full /home/margaret/Data/dbSNP/grch37/dbSNP_grch37.vcf | ./vt normalize -r /home/margaret/Data/dbSNP/grch37/human_g1k_v37.fasta - | ./vt uniq -o dbsnp_grch37_normalized.vcf - &


Here is my output:

margaret@SII-T7500-01:~/Programs/vt$ normalize v0.5

options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency false [q] quiet false [d] debug false [r] reference FASTA file /home/margaret/Data/dbSNP/grch37/human_g1k_v37.fasta

uniq v0.57

options: input VCF file -

[o] output VCF file dbsnp_grch37_normalized.vcf

[variant_manip.cpp:96 is_not_ref_consistent] reference bases not consistent: Y:10019-10019 T(REF) vs N(FASTA)

[normalize.cpp:209 normalize] Normalization not performed due to inconsistent reference sequences. (use -n or -m option to relax this)

[W::vcf_parse] INFO 'db' is not defined in the header, assuming Type=String

stats: Total number of observed variants 149043129 Total number of unique variants 147668200

Time elapsed: 8m 23s

grch37 dbsnp vt normalization vcf • 1.5k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by plink_985750
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