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| ====Outputs==== | | ====Outputs==== |
| Upon successful completion of the *recab* sub-pipeline, you should see the following files/subdirectories under the user specified output directory: | | Upon successful completion of the *recab* sub-pipeline, you should see the following files/subdirectories under the user specified output directory: |
− | *'''recab/mergedBams/''' | + | *'''recab/mergedBams/''' - contains merge results |
| ** '''''*/SAMPLE.merged.bam'' - a merged BAM file''' | | ** '''''*/SAMPLE.merged.bam'' - a merged BAM file''' |
| ** ''*/SAMPLE.merged.bam.log'' - merge log | | ** ''*/SAMPLE.merged.bam.log'' - merge log |
| ** ''*/SAMPLE.merged.bam.OK'' - temp file indicating the merge step completed successfully | | ** ''*/SAMPLE.merged.bam.OK'' - temp file indicating the merge step completed successfully |
| | | |
− | * '''recab/''' | + | * '''recab/''' - contains recalibration results |
| ** '''''*/SAMPLE.recal.bam'' - a merged, recalibrated, and deduped BAM file''' | | ** '''''*/SAMPLE.recal.bam'' - a merged, recalibrated, and deduped BAM file''' |
| ** '''''*/SAMPLE.recal.bam.bai'' - an indexed version of the merged, recalibrated, and deduped BAM file''' | | ** '''''*/SAMPLE.recal.bam.bai'' - an indexed version of the merged, recalibrated, and deduped BAM file''' |
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| ** ''*/SAMPLE.recal.bam.done'' - temp file indicating the recalibration step completed successfully | | ** ''*/SAMPLE.recal.bam.done'' - temp file indicating the recalibration step completed successfully |
| ** ''*/SAMPLE.recal.bam.bai.done'' - temp file indicating the indexing step completed successfully | | ** ''*/SAMPLE.recal.bam.bai.done'' - temp file indicating the indexing step completed successfully |
| + | |
| + | * '''QCFiles/''' - contains quality control results |
| + | ** VerifyBamID Output - see [[VerifyBamID#A_guideline_to_interpret_output_files|VerifyBamID: A guideline to interpret output files]] for more information |
| + | *** *.genoCheck.depthRG - depth distribution of the sequence reads per read group |
| + | *** *.genoCheck.depthSM - depth distribution of the sequence reads per sample |
| + | *** ''*.genoCheck.done'' - temp file indicating this step completed successfully |
| + | *** *.genoCheck.selfRG - per-readGroup statistics describing how well each lane matches to the annotated sample |
| + | *** '''*.genoCheck.selfSM''' - main output file containing the contamination estimate; per-sample statistics describing how well the sample matches to the annotated sample |
| + | **** Check the 'FREEMIX' column for genotype-free estimate of contamination 0-1 scale, the lower, the better |
| + | **** If [FREEMIX] >= 0.03 and [FREELK1]-[FREELK0] is large, possible contamination |
| + | ** Qplot Output - see: [[QPLOT#Diagnose_sequencing_quality|QPLOT: Diagnose sequencing quality]] for more info on how to use QPLOT results |
| + | *** ''*.qplot.done'' - temp file indicating this step completed successfully |
| + | *** '''*.qplot.R''' - Rscript that can be used to generate the pdf graphs |
| + | *** '''*.qplot.stats''' - sample statistics |
| + | |
| You should see .done and .OK files for each SAMPLE in the index file. If you do not see the .done and .OK files, then your *recab* sub-pipeline failed. | | You should see .done and .OK files for each SAMPLE in the index file. If you do not see the .done and .OK files, then your *recab* sub-pipeline failed. |
| | | |