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Fix typos #126

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merged 5 commits into from
Feb 25, 2020
Merged

Fix typos #126

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77d0ea6
update docs
maxulysse Feb 24, 2020
d984a14
fix path in iGenomes for Mouse
maxulysse Feb 24, 2020
3f4d25c
Merge branch 'dev' into FixLink
maxulysse Feb 24, 2020
64ac0a3
fix paths
maxulysse Feb 24, 2020
0d5fa6e
Merge branch 'FixLink' of github.com:MaxUlysse/sarek into FixLink
maxulysse Feb 24, 2020
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8 changes: 4 additions & 4 deletions conf/igenomes.config
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Expand Up @@ -53,14 +53,14 @@ params {
bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
chr_dir = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Chromosomes"
chr_length = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Length/GRCm38.len"
dbsnp = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/Annotation/mgp.v5.merged.snps_all.dbSNP142.vcf.gz"
dbsnp_index = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/Annotation/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi"
dbsnp = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz"
dbsnp_index = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi"
dict = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.dict"
fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
fasta_fai = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa.fai"
intervals = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/intervals/GRCm38_calling_list.bed"
known_indels = "${params.igenomes_base}/Mus_musculus/Annotation/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz"
known_indels_index = "${params.igenomes_base}/Mus_musculus/Annotation/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
known_indels = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz"
known_indels_index = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
snpeff_db = 'GRCm38.86'
species = 'mus_musculus'
vep_cache_version = '98'
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10 changes: 5 additions & 5 deletions docs/input.md
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Expand Up @@ -5,15 +5,15 @@
Input files for Sarek can be specified using a TSV file given to the `--input` command.
The TSV file is a Tab Separated Value file with columns:

- `subject gender status sample lane fastq1 fastq2` for step `mapping` with paired-end FASTQs
- `subject gender status sample lane bam` for step `mapping` with unmapped BAMs
- `subject gender status sample bam bai recaltable` for step `recalibrate` with BAMs
- `subject gender status sample bam bai` for step `variantcalling` with BAMs
- `subject sex status sample lane fastq1 fastq2` for step `mapping` with paired-end FASTQs
- `subject sex status sample lane bam` for step `mapping` with unmapped BAMs
- `subject sex status sample bam bai recaltable` for step `recalibrate` with BAMs
- `subject sex status sample bam bai` for step `variantcalling` with BAMs

The content of these columns is quite straight-forward:

- `subject` designate the subject, it should be the ID of the Patient, and it must design only one patient
- `gender` is the gender of the Patient, (XX or XY)
- `sex` are the sex chromosomes of the Patient, (XX or XY)
- `status` is the status of the Patient, (0 for Normal or 1 for Tumor)
- `sample` designate the Sample, it should be the ID of the sample (it is possible to have more than one tumor sample for each patient, i.e. a tumor and a relapse), it must design only one sample
- `lane` is used when the sample is multiplexed on several lanes, it must be unique for each lane in the same sample
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