giraffe alignment for exome sequencing
Is there a way to restrict alignment to exome regions only? When I use normal alignment (./vg giraffe -p -Z "$gbz_file" -m "$min_file" -d "$dist_file" -f "$file1" -f "$file2" > "$output_filename" .) on vg version v1.50.1, I get a lot of single reads mapped to non-exome regions. I also get very long variants that include both exome and non-exome regions that I don't know how to interpret in light to the fact that it is only based on exome reads.
Any help in understanding this ?
• 571 views
•
link
updated
by
Ram
•
written
by
Michal Frenkel •
•
written
by
Michal Frenkel •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Is vg giraffe appropriate for RADseq sequencing reads?
written by RianeZ •
-
Does vg giraffe output secondary and supplimentary alignments?
written by lushjia •
-
warning[vg::giraffe]: Cannot cluster reads with a fragment distance smaller than read distance
written by cassiwatt •
-
Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject
written by cassiwatt •
-
How to obtain full alignment results?
written by nrqstudent •
-
very long variants in VCF after giraffe alignment
written by Michal Frenkel •
-
HiFi read alignment with vg giraffe
written by shehzad_99 •
-
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to con…
written by Maxine •
-
Retrieving alignment scores with vg surject
written by Gabriela •
-
Venn Diagram for 3 BEd files
written by Lila M
