mwadswor
commented
8 years ago I am having this same problem. I tried to import the file as described in the above post, but I am not able to access any insertions. They are there when I pull up the variant using the region command. I am just using the provided example file. I can find deletions just fine, just not insertions.
lh3
I am trying to find insertions using the -a,#variant# framework but I can't get it to return anything. Deletions and SNPs work fine with this format, but insertions always return null. I've tried many variations of the formatting. I even tried to find insertions using the variant IDs generated by the vep2sql.js (using the -f flag) script, but even these return null. Searching for these same variants using the -r region flag works perfectly, so I know they exist in the database. Any help? I don't think its an error with my formatting and it seems limited to insertions.
For example:
This is a variant identified by VEP running the 1kg11-1M.raw.bcf with the following command:
"variant_effect_predictor.pl -i 1kg11-1M.raw.vcf -o 1kg11-1M.raw.vcf.vep --refseq --dir /home/ec2-user/.vep --offline --pick --cache --everything --force_overwrite"
The output was processed through vep2sql.js:
"k8-linux bgt/misc/vep2sql.js -f 1kg11-1M.raw.vcf.vep > 1kg11-1M.raw.vcf.vep.fmf"
Running "bgt view -t CHROM,POS,REF,ALT -a,11:607967:0:CTCCGA 1kg11-1M.bgt" (the allele found in the 1kg11-1M.raw.vcf.vep.fmf file) returns nothing.
However, running "bgt view -t CHROM,POS,REF,ALT -a,11:608013:1:A 1kg11-1M.bgt" (the next allele on the list) does work.
Finding the insertion via searching the region does function and finds the variant.
bgt view -t CHROM,POS,REF,ALT -r 11:607960-607970 1kg11-1M.bgt