wjaratlerdsiri

Dear Author, I made hg38 reference using Tandem Repeats Finder (./trf409.macosx Homo_sapiens_assembly38.fasta 2 7 7 80 10 50 500 -f -d -m). At the end, I got about 237,302 STRs...

Got a new problem? wget https://pypi.python.org/packages/source/P/PyVCF/PyVCF-0.6.7.tar.gz tar -zxvf PyVCF-0.6.7.tar.gz $ /bcbiometasv/miniconda/bin/python2.7 setup.py build /bcbiometasv/miniconda/bin/python2.7 setup.py install --prefix /bcbiometasv/miniconda creating /bcbiometasv/miniconda/lib/python2.7/site-packages/PyVCF-0.6.7-py2.7-linux-x86_64.egg Extracting PyVCF-0.6.7-py2.7-linux-x86_64.egg to /bcbiometasv/miniconda/lib/python2.7/site-packages Adding PyVCF 0.6.7 to easy-install.pth file...

Hang on Marghoob! When I submitted my job via qsub, the job above is still running until now, March 2nd 8am. I am sure because I have checked spades.log file....

THX for the follow-up, I have to do other projects, so I moved BAM file away. I will try soon. However, if performing only merging, it worked well. I am...

Sample file of Lumpy+SVtyper: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT UP chr1 569387 6 N 0.00 . SVTYPE=DEL;SVLEN=-457;END=569844;STRANDS=+-:7;CIPOS=-5,4;CIEND=-6,4;CIPOS95=0,0;CIEND95=0,0;SU=7;PE=0;SR=7 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:RP:AP:AB 0/0:7:0:7:134.86:0.00:-84,-27765,-94585:96182:95754:428:95753:427:37686:14:58067:413:0.0044 0/0:0:0:0:200:0.00:-8,-3339,-11423:11654:11589:64:11589:63:0:0:11589:63:0.0054 chr1 991719 9 N 12.39 ....