From Genome Analysis Wiki
Jump to navigationJump to search
713 bytes added
, 00:05, 18 June 2014
Line 252: |
Line 252: |
| | | |
| [[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 == |