Hi,
I have a tab delimited file with GWAS results and I am trying to annotate the variants using Annovar but my format for INDELS is different, and I get my indels split between the invalid_input, where I find these SNPs in my file:
1 63735 63735 CCTA C
1 251627 251627 AC A
1 760811 760811 CTCTT C
While they should be like this:
1 63735 CCTA 4C 0.339 rs201888535
1 251627 AC 2A 0.172 rs72502741
1 760811 CTCTT 5C 0.0417 rs200712425
and some in the "filtered" file like this:
1 36549207 36549207 A ACT
which are in Annovar like this:
1 36549207 A 0CTC 0.9076 rs143406521
1 36549207 A 1ACTC 0.9076 rs143406521
I am wondering what is the best way to convert these formats, and if there is a standard way/a script to do this as I am afraid to get it wrong and convert only insertions and not deletions or the opposite... thanks so much for your help.
1 answer
ANNOVAR website provides instructions on preparing VCFs:
So as a user, this is what you should do: (1) split VCF lines so that each line contains one and only one variant (2) left-normalize all VCF lines (3) annotate by ANNOVAR.
For example, suppose the input is ex1.vcf.gz (make sure that it is processed by bgzip and then by tabix), this is what you would do:
bcftools norm -m-both -o ex1.step1.vcf ex1.vcf.gz
bcftools norm -f human_g1k_v37.fasta -o ex1.step2.vcf ex1.step1.vcf
The first command split multi-allelic variants calls into separate lines, yet the second command perform the actual left-normalization. The FASTA file is needed in the second command.
Source: http://annovar.openbioinformatics.org/en/latest/articles/VCF/
I didn't realize you don't have a VCF at all. Not sure how you can do this with a custom format. My first suggestion would be to create a VCF file, but I am not sure how easy it would be, especially with indels. Some options here: bed to vcf format conversion
Sorry @igor I tried your tip for using ANNOVAR about INDELS but I am getting this error
[fi1d18@cyan01 annovar]$ bcftools norm -f hs37d5.fa -o ex1.step2.vcf ex1.step1.vcf [fai_fetch_seq] The sequence "chr1" not found
faidx_fetch_seq failed at chr1:1499775
[fi1d18@cyan01 annovar]$
But I don't know what does that mean
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