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iobio / vcf.iobio.io

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Variant density dropoff shown as slope for genome (all references) view. #27

Closed tonydisera closed 8 years ago

tonydisera commented 8 years ago
screenshot 2016-06-03 11 21 37
tonydisera commented 8 years ago

use test file: https://s3.amazonaws.com/iobio/app_testing/vcf_files/no_af_indels_qual.vcf.gz

AlistairNWard commented 8 years ago

Not sure if this is the same problem or not, but there is something odd going on around chr20-23. There is a line being drawn behind the density.

Also, are we happy with just numerical values for all chromosomes? For the human genome, we are going to want to see X and Y, not 23 and 24.

tonydisera commented 8 years ago

Taking a closer look at the density data, there is something strange going on with chr 20. The density data has points through ~ 130,500,000, but the chromosome is only 63,000,000. I wonder if the index needs to be re-generated for this file or if we are perhaps seeing the problem of an out-dated index file....

The other oddity is the chromosomes listed. Rather than ending at 26 (with 25=X,26=Y), there are 29 chromosomes listed that don't seem to map to the correct chromosome lengths.