Submitter: Owen Miller Email: o.miller@se17.qmul.ac.uk Hi, I'm using Meerkat as part of my masters project to map structural variants within cancer genomes. I'm having issues with the filtering step: I always get an empty (0 byte) file as the output. Having manually inspected my .variants output files, I can identify positions shared between my normal sample and my tumor samples, but the filtering script isn't giving me any output at all.

Here's the script i'm running:

somatic_sv.pl \ -i /data/BCI-EvoCa2/owen/07_Meerkat/Results/Polyp.08.WGS/Polyp_8A/run_2/Polyp_8A.mkdub.variants \ -o /data/BCI-EvoCa2/owen/07_Meerkat/Results/Polyp.08.WGS/Polyp_8A/run_2/Polyp_8A.mkdub.somatica.variants \ -F /data/BCI-EvoCa2/owen/07_Meerkat/Results/Polyp.08.WGS/Polyp_8Normal/run_2 \ -R /data/BCI-EvoCa2/owen/reference_genome_hg19/RepeatMasker_refGene_hg19.txt.gz

Here is the steps I ran before this point:

pre_process.pl \ -b Polyp_8A.mkdub.bam \ -I /data/BCI-EvoCa2/marc/refs/hg19/ucsc.hg19.fasta \ -A /data/BCI-EvoCa2/marc/refs/hg19/ucsc.hg19.fasta.fai \ -k 1500 \ -t 10 \ -s 20 \ -q 15 \ -l 0

replace sample blacklist.gz with normal blacklist.gz

rm Polyp_8A.mkdub.blacklist.gz ln -s /data/BCI-EvoCa2/owen/07_Meerkat/Results/Polyp.08.WGS/Polyp_8Normal/run_2/Polyp_8Normal.mkdub.blacklist.gz Polyp_8A.mkdub.blacklist.gz

meerkat.pl \ -b Polyp_8A.mkdub.bam \ -F /data/BCI-EvoCa2/marc/refs/hg19/ \ -m 0 \ -t 10 \ -s 20 \ -d 5 \ -p 3 \ -o 1 \ -l 0

mechanism.pl \ -b Polyp_8A.mkdub.bam \ -R /data/BCI-EvoCa2/owen/reference_genome_hg19/RepeatMasker_refGene_hg19.txt.gz

Any idea as to why I might not be getting any output from the filtering step?

parklab / Software-Issues

Meerkat somatic_sv.pl issues #15

replace sample blacklist.gz with normal blacklist.gz