NationalGenomicsInfrastructure/ngi_pipeline

Autosomal coverage in Charon

Closed this issue · 6 comments

parlundin commented

Autosomal coverage not updated in Charon.
Before when it worked it was calculated a bit wrong. Is that fixed?

mariogiov commented

I'll check this out

mariogiov commented

Okay so autosomal coverage is updated in Charon, except for this particular project we discussed. The issue of the naive averaging I believe persists however. We can fix this pretty easily as we discussed.

vezzi commented

I take the "naive averaging" comment personally :-D

Galithil commented

some projects still marked as running on charon are not in the tracking db. I am not sure why.

Galithil commented

It looks like the pipeline tres to mark seqruns as "analyzed". That won't work. I pushed a fix to the current PR we are having.

mariogiov commented

Just so I have it written down somewhere, the data we're looking for resembles:

>>>>>>> Coverage per contig

        1       249250621       7838672256      31.448957778123248      1102.2335967799827
        2       243199373       8169441537      33.59154029151218       178.53134983206547
        3       198022430       6406746456      32.3536402214638        27.481348469645315
        4       191154276       6583671042      34.44166240884928       325.1054489022348
        5       180915260       5868639181      32.43860789299919       16.164412264854395
        6       171115067       5612646141      32.80042043872151       136.6088468013857
        7       159138663       5227965007      32.85163333941043       312.82741785987895
        8       146364022       4838993675      33.0613603594468        274.995856394256
        9       141213431       3974294677      28.14388581069176       188.96715674627475
        10      135534747       5061628961      37.345618544593584      728.1048800375078
        11      135006516       4363653997      32.321802875055305      203.14337081163242
        12      133851895       4229032326      31.594863307687948      30.652726688489658
        13      115169878       3158773865      27.427083538284204      14.239201313093492
        14      107349540       2862689948      26.666997809212784      17.705910207934615
        15      102531392       2634469062      25.69426797599705       18.48471359915318
        16      90354753        2801463669      31.005161056662953      190.79223022049916
        17      81195210        2528671360      31.14311004306781       205.3748487767622
        18      78077248        2571290204      32.93264388621894       213.32223934723373
        19      59128983        1774962064      30.018477808082714      512.3188008255823
        20      63025520        1903226721      30.197715480967076      63.67997854327818
        21      48129895        1283817814      26.674020668443177      89.17765001475064
        22      51304566        1040898484      20.288612986220368      21.628760843389077
        X       155270560       5095162791      32.81473829295135       80.35260264634742
        Y       59373566        172492404       2.905205390560506       231.74300886545285
        MT      16569   41967703        2532.905003319452       172.9416357371165

Where we want to report as coverage sum(column_3) / sum(column_2) (omitting X, Y, and MT).