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Revision as of 22:23, 16 March 2015
, 22:23, 16 March 2015→recab
This sub-pipeline takes in a single, recalibrated BAM file, creates an index file for it, and performs quality control (running qplot and verifyBamID). It differs from *bamQC* in that it does not require that the user already have a .bai file for the recalibrated BAM file.
This sub-pipeline takes in a single, recalibrated BAM file, creates an index file for it, and performs quality control (running qplot and verifyBamID). It differs from *bamQC* in that it does not require that the user already have a .bai file for the recalibrated BAM file.
== recab ==
== recab ==
*What it does:
# merge BAMs for samples that have multiple BAMs
# dedup and recalibrate
# index the recalibrated BAM
====Inputs====
* Bam files (stored in a [[#BAM_LIST|BAM_LIST]] file)
* Reference files
* (Optional) configuration file to override default options
=====BAM_LIST File=====
* Each line of the BAM list file represents a single individual
Columns:
# sample id
# comma separated population labels (optional column)
# BAM File 1 (preferable to have full paths to BAM files)
# BAM File 2 (if more than 1 BAM per sample)
:...
: # BAM File N (if more than 1 BAM per sample)
[SAMPLE_ID] [COMMA SEPARATED POPULATION LABELS] [BAM_FILE1] [BAM_FILE2] ...
or
[SAMPLE_ID] [BAM_FILE1] [BAM_FILE2] ...
* Notes:
** tab delimited
** multiple BAMs per individual may be provided, but should all be on the same line of the list file
** population label is optional - it will default to <code>ALL</code>
*** only used by Thunder (part of ldrefine pipeline)
*** if all samples are from the same population, population label can be skipped or you can just specify <code>ALL</code> for the population label for each sample.
====Outputs====
Upon successful completion of the *recab* sub-pipeline, you should see the following files/subdirectories under the user specified output directory:
*'''recab/mergedBams/'''
** '''''*/SAMPLE.merged.bam'' - a merged BAM file'''
** ''*/SAMPLE.merged.bam.log'' - merge log
** ''*/SAMPLE.merged.bam.OK'' - temp file indicating the merge step completed successfully
* '''recab/'''
** '''''*/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.metrics'' - dedup & recalibration log
** ''*/SAMPLE.recal.bam.qemp'' - recalibration tables
** ''*/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
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.
'''On success, the recab/ folder contains the final BAMs and bais.'''
===Command-Line and Configuration Options===
*Required Options
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
| --list/--bam_list/--bamlist ''file'' || BAM_LIST || path to the [[#BAM_LIST File|BAM_LIST File]] || $(OUT_DIR)/bam.list
|-
| --numjobs ''#'' || || number of jobs to run in parallel || 0 (generate Makefile of steps, but do not run)
|}
*Common Options
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! colspan="4" | Common Options
|-
! Command-line Flag !! Configuration Key !! Value Description !! Default Value
|-
| --outdir ''path'' || OUT_DIR || output directory ||
|-
| --conf ''file'' || || configuration file to use ||
|-
| || REF_DIR || where the reference/resource files are stored || gotcloud.ref subdirectory within the base GotCloud directory
|-
| || REF || [[GotCloud: Genetic Reference and Resource Files#Reference fasta Files|Reference fasta Files]] || $(REF_DIR)/human.g1k.v37.fa
|-
| || DBSNP_VCF || [[GotCloud: Genetic Reference and Resource Files#DBSNP VCF Files|DBSNP VCF Files]] || $(REF_DIR)/dbsnp_135.b37.vcf.gz
|}
==== Example Configuration File ====
Example configuration file where reference files happen to be stored in /path/reference, and bam list file is stored in in path/freeze5
BAM_LIST = /path/freeze5.bam.list
OUT_DIR = /path/freeze5/output
REF_DIR = /path/reference/
REF = $(REF_DIR)/hs37d5.fa
DBSNP_VCF = $(REF_DIR)/dbsnp_135.b37.sites.vcf.gz
==== Example Command Line ====
gotcloud pipe –-name recab --numjobs <N>
== recabQC ==
== recabQC ==
