Deletions Too Big

I’ve noticed sometimes both addindel.py and addsv.py will make deletions that are larger than what’s specified.

For example, calling python $addindel -v $indels -f $originalBam -p 8 -d 0 -r $fasta --picardjar $picardjar --aligner mem --insane -o $indelBam with $indels:

22      38827224        38827245        0.5     DEL

results in a deletion almost 2kb (should be 21bp):

The log file looks normal: a list of 20 reads, then

indel   DEL:22:38827224:38827245        38827224        FIX get_mutstr  19.0416666667   16.0416666667   0.5     0.0

Is this a known issue?

[adamewing]

Sorry for the delay in responding - what you’re running into is that addsv doesn’t specify mutations exactly: the chromosome/start/stop coordinates in the variant input file define regions where addsv will attempt to make a contig and the other fields are information about the type of mutation you’re trying to make. The exact coordinates of the breakpoints will be defined in the truth file e.g. generated with the included makevcf_sv script.

[charliecurnin]

I don’t think my modification changed it’s behavior: though maybe I should have just changed the condition on 522 to if len(a) > a and a[1] != "-1".