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tk2 / RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
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hets option for the calling phase #20

Closed Milad021 closed 5 years ago

Milad021 commented 5 years ago

Dear Mr. Keane,

I am currently analyzing about 50 samples and I have used the -hets option. However in the end, by analyzing my vcf file I only find homozygotes.

I have ran the following command :

retroseq.pl -call -depth 10000 -reads 3 -q 30 -hets -bam $path_bam_file -input candidats.tab -ref /data/UMD3_1.fa -filter /data/types.tab -output sample_HET.vcf

> 1/1:20:8:0:4:3 (in my vcf file).

In my other samples I only find homozygotes instead of heterozygotes like 1/1. Is this normal?

Best reagards,

Milad

tk2 commented 5 years ago

Hi - the -hets option is not active in the current version. I added it to an earlier version and found after testing that it didn't work very well, so I removed it until the accuracy could be improved.

Rgds, Thomas