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Revision as of 00:05, 18 June 2014
, 00:05, 18 June 2014→Running GotCloud/GenomeSTRiP Discovery Pipeline
[[File:Genomestrip discovery screenshot.png|800px]]
[[File:Genomestrip discovery screenshot.png|800px]]
=== How many variants are filtered out? ===
Run the following command to see filtering statistics.
grep -v ^# $OUT/sv/discovery/discovery.vcf | cut -f 7 | sort | uniq -c
You will see the following output
7 COHERENCE;COVERAGE;DEPTH;DEPTHPVAL
17 COHERENCE;COVERAGE;DEPTH;DEPTHPVAL;PAIRSPERSAMPLE
3 COHERENCE;COVERAGE;DEPTH;PAIRSPERSAMPLE
2 COHERENCE;COVERAGE;DEPTHPVAL;PAIRSPERSAMPLE
1 COHERENCE;COVERAGE;PAIRSPERSAMPLE
3 COVERAGE
1 COVERAGE;DEPTH
67 COVERAGE;DEPTH;DEPTHPVAL
270 COVERAGE;DEPTH;DEPTHPVAL;PAIRSPERSAMPLE
2 COVERAGE;DEPTH;PAIRSPERSAMPLE
4 COVERAGE;DEPTHPVAL
5 COVERAGE;DEPTHPVAL;PAIRSPERSAMPLE
5 COVERAGE;PAIRSPERSAMPLE
== Run GotCloud SnpCall ==
== Run GotCloud SnpCall ==
