mtDNA deletion not called

[1ctw]

I have found a large deletion in mtDNA in case 25342 but it is not called by TIDDIT.

It would be good if you looked a little closer at the reason why it´s not called.

[dnil]

Yes, that is a pretty clean del. Passing it on to @J35P312 and @jemten for starters perhaps.

I note, not without satisfaction, that the little samtools oneliner for discordant reads still does good:

Given that normal values are very near 0, and a ratio of 5ppk it would have fit in the top 10 among the del test cases. 😊

[jemten]

Discussed this briefly with @J35P312 and he pointed out that for the left breakpoint all the supporting reads had a MQ of 0 which is probably why tiddit fails, it disregards those reads. That and the little peak right before the breakpoint could indicate some sort of insertion happening as well.

[dnil]

Nice! Might be of some interest to realign the sample to 38? It looks like those "insertion" sequences on the right flank kind of match a part of the chr1 subtelomere in hg38.

[jemten]

True! We can put it on the list of samples to try with 38. Would also be interesting to try running MitoSalt for this case, which @ieduba is currently evaluating for mitochondrial deletions.

[1ctw]

Sounds good! @ieduba run the MitoSalt analysis already yesterday with a very nice result:)

[jemten]

Sounds good! @ieduba run the MitoSalt analysis already yesterday with a very nice result:)

Nice! Then we look forward to integrating that in the pipeline 😄