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Minor changes to options.
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@sebastianlange
sebastianlange committed Jul 19, 2019
1 parent 3ef52d1 commit 1fa174b
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6 changes: 3 additions & 3 deletions MoCaSeq.sh
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Expand Up @@ -11,7 +11,7 @@
usage()
{
echo " Usage: $0 "
echo " -n, --name Name of the sample"
echo " -n, --name Name of the sample."
echo " -nf, --fastq_normal_fw Path to first normal Fastq. Do NOT use if running single-sample tumor only."
echo " -nr, --fastq_normal_rev Path to second normal Fastq. Do NOT use if running single-sample tumor only."
echo " -tf, --fastq_tumor_fw Path to first tumor fastq. Do NOT use if running single-sample normal only."
Expand All @@ -21,12 +21,12 @@ usage()
echo " -rm, --repeat_mapping If -nb or -tb are specified, determines whether mapping is re-done ('yes') or whether the complete mapping procedure is skipped ('no')."
echo " -st, --sequencing_type Set to 'WES' or 'WGS'. Defaults to WES."
echo " -c, --config Path to configuration file. Optional."
echo " -qc, --quality_control Determines wheter QC is done ('yes') or skipped ('no'). Optional."
echo " -qc, --quality_control Determines whether QC is done ('yes') or skipped ('no'). Optional."
echo " -t, --threads Number of CPU threads. Optional. Defaults to 8."
echo " -r, --ram Amount of Gb RAM. Optional. Defaults to 32."
echo " -temp, --temp_dir Path to temporary directory. Optional. Defaults to current working directory."
echo " -art, --artefact Set to 'GT' (oxidation artefact), 'CT' (FFPE artefact) or 'none'. Optional. If set to something other than 'none' AND Mutect2 is 'yes', forces quality_control to 'yes'. Defaults to none."
echo " -filt, --filtering Set to 'all' (AF >= 0.05, Variant in Normal <= 1, Coverage >= 5), 'hard' (AF >= 0.1, Variant in Normal = 0, Coverage >= 10) or 'none' (no filters). Optional. Defaults to 'hard'"
echo " -filt, --filtering Set to 'all' (AF >= 0.05, Variant in Normal <= 1, Coverage >= 5), 'hard' (AF >= 0.1, Variant in Normal = 0, Coverage >= 10) or 'none' (no filters). Optional. Defaults to 'hard'."
echo " -p, --phred If not set, script will try to automatically extract phred-score. Otherwise, set manually to 'phred33' or 'phred64'. 'phred64' only relevant for Illumina data originating before 2011. Optional."
echo " -mu, --Mutect2 Set to 'yes' or 'no'. Needed for LOH analysis and Titan. Greatly increases runtime for WGS. Optional. Defaults to 'yes'."
echo " -de, --Delly Set to 'yes' or 'no'. Needed for chromothripsis inference. Do not use for WES. Optional. Defaults to 'no'. Only use in matched-sample mode."
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -86,7 +86,7 @@ This will run the pipeline with your current UID and GID and set the permissions
### Options
| short | long | Details |
|-------|--------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| -n | --name | Name of the sample |
| -n | --name | Name of the sample. |
| -nf | --fastq_normal_fw | Path to first normal Fastq. Do NOT use if running single-sample tumor only. |
| -nr | --fastq_normal_rev | Path to second normal Fastq. Do NOT use if running single-sample tumor only. |
| -tf | --fastq_tumor_fw | Path to first tumor fastq. Do NOT use if running single-sample normal only. |
Expand All @@ -96,7 +96,7 @@ This will run the pipeline with your current UID and GID and set the permissions
| -rm | --repeat_mapping | If -nb or -tb are specified, determines whether mapping is re-done ('yes') or whether the complete mapping procedure is skipped ('no'). |
| -st | --sequencing_type | Set to 'WES' or 'WGS'. |
| -c | --config | Path to configuration file. Optional. |
| -qc | --quality_control | Determines wheter QC is done ('yes') or skipped ('no'). Optional. |
| -qc | --quality_control | Determines whether QC is done ('yes') or skipped ('no'). Optional. |
| -t | --threads | Number of CPU threads. Optional. Defaults to 8. |
| -r | --ram | Amount of Gb RAM. Optional. Defaults to 32. |
| -temp | --temp_dir | Path to temporary directory. Optional. Defaults to current working directory. |
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