chanjo

chanjo copied to clipboard

Raise warning if sex prediction is based on too few exons

1

Set a reasonable cutoff for how many exons the prediction is based on (X/Y)

robinandeer

Update bootstrap to select between GRCh37/38

3

Latest CCDS is based on GRCh38

robinandeer

henrikstranneheim

Does it exclude reads located with bp position = bp2: - 'b36'/'hg18' = NCBI 36, 2709521/154584237 - 'b37'/'hg19' = GRCh37, 2699520/154931044 - 'b38'/'hg38' = GRCh38, 2781479/155701383

henrikstranneheim

Store expected sex of sample

2

- compare in report - read in ped file? @moonso

robinandeer

This is a first very simple example: ``` python def gc_content(self, query=None, gc_amount='high', gene_ids=None): """Generate query to estimate coverage performace. Works by default on a small subset of genes with...

robinandeer

It would be nice to get a "clean" log file for each process call to avoid looking at old error messages

henrikstranneheim

Capture sambamba output and pipe to logfile

4

If one runs sambamba through chanjo it would be awesome if the STDOUT/ERR would redirect to the same logfiles, don't you think?

robinandeer

If the coverage-limit set has something to do with the measurement of 'Fullständighet' it would be good to have it in the explanation. The text in the report below: 'Fullständighet:...

emmser

Make `load_sambamba` return created sample objects

robinandeer