Hey, anyone here experienced with HTSJDK?
I'm currently using it to read VCF files (bi-allelic microarray derived) and grab all the genotypes for all the individuals then transform them into a Byte Array, storing each genotype as the sum of it's indices (so ./. > -2, 0/0 > 0, 0/1 > 1, 1/1 > 2 etc). Using other language (cyvcf2 etc) libraries they often natively provide genotypes as indices. However, with HTSJDK when requesting genotypes from a VariantContext with getGenotypes() you get the genotypes in base form (something like [A*, C], [A*, A*], [C, C] where each allele is it's own object). Currently I'm using getAlleleIndices() from VariantContext to convert these Genotype objects back into an Array of indices which I can then sum. This is a bit slower than I'd ideally like, as such is there a better or faster way of doing this rather than using getAlleleIndices() to transform each Genotype into it's Indices?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
Latest Articles
Collapse
-
by seqadmin
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
Channel: Articles
07-08-2024, 03:19 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:46 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:46 AM
|
||
Started by seqadmin, 07-24-2024, 11:09 AM
|
0 responses
26 views
0 likes
|
Last Post
by seqadmin
07-24-2024, 11:09 AM
|
||
Started by seqadmin, 07-19-2024, 07:20 AM
|
0 responses
160 views
0 likes
|
Last Post
by seqadmin
07-19-2024, 07:20 AM
|
||
Started by seqadmin, 07-16-2024, 05:49 AM
|
0 responses
127 views
0 likes
|
Last Post
by seqadmin
07-16-2024, 05:49 AM
|