No clipping read counts?

[Yeonghun lee]

Hello,

I have tried to use the qSV tool, which seems to successfully find SVs in TCGA samples.

However, I have failed obtaining clipping read "counts", even though the output showed some SVs that were definitely supported by clipping reads (tagged with category 2).

analysis_id sample_id sv_id sv_type chr1 pos1 strand1 chr2 pos2 strand2 test_discordant_pairs_count control_discordant_pairs_count control_low_qual_discordant_reads_count test_clips_count_pos1 test_clips_count_pos2 control_clips_count_pos1 control_clips_count_pos2 category microhomology non-template test_split_read_bp control_split_read_bp event_notes contig

TCGAsample tumor sm_109 DUP/INS/ITX 8 55968427 + 8 54357006 + 25 0 0 0 0 0 0 2 GCA not found 2 | 8: 55968427 | 8:54357006 GACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGGACAAAAAACCAAACACCGCATGTTCTCACTCATAGCTGGGAATTGAACAATGAGAACACTTGGACACAGGAAGGGGAACATCACAATCTGGGGACTCTTGTGGGGTGGGGGGAGGGGGGAGGGATAGCAAAG TATAGAAAACCTTGGCAAAATTAACGTTCTAAATTGATTGAGACCTGTCTCAGATACTTTTGGTTTACATATCTAAGGATAAATTCCC

I was fine when I was working with other samples (not TCGA).

[Ollie Holmes]

Hi Yeonghun,
Thanks for your post.
You have identified a bug within qSV relating to the way in which breakpoints are identified. The code was expecting contigs to start with "chr", which may be why it works for some samples and not others.
I've put a fix in place and we are testing the new code internally. Once we are happy with it, I'll send you a copy of the updated jar.
Thanks again for spotting this!
Cheers,
Ollie

[Yeonghun lee]

Hi Ollie,
I really thank you for your consideration.
I usually analyze TCGA samples mapped to GRCh37, which uses contig names without "chr".
Unfortunately, It would be time-consuming to change contig names across all the samples.
I hope to use qSV for TCGA samples as soon as possible.
Cheers!
Yeonghun

[Ollie Holmes]

Hi Yeonghun,
I've placed a new qsv tar file on the downloads page called qsv-0.3.tar.bz2.
This version should contain the fixes that you require to run your data.
Please let me know if you continue to have issues.
Many thanks and apologies for the huge delay...
Oliver