Description Usage Arguments Value
a single slurm job. help doc: https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | run_GBSv2(outdir = "largedata/gbs", shfile, fqdir, keyfile, bt2_idx, sam,
ref, snpqc_file, h5, db = NULL, mem, cpu, kmerlen = 64,
enzyme = "ApeKI", mnlcov = 0.05, mnmaf = 0.01,
deleteolddata = "true", production = FALSE, seq2tag = TRUE,
tag2fq = TRUE, bt2 = TRUE, snpcall = TRUE)
GBSSeqToTag(shfile, mem, fqdir, db, keyfile, kmerlen, enzyme)
TagExportToFastq(shfile, mem, db, tagexport, mindepth = 1)
run_bowtie2(shfile, cpu, bt2_idx, tagexport, sam)
SAMToGBSdb(shfile, mem, sam, db)
DiscoverySNP(shfile, mem, db, ref, mnlcov = 0.05, mnmaf = 0.001,
deleteolddata)
SNPQuality(shfile, mem, db, snpqc_file)
ProductionSNPCaller(shfile, mem, db, enzyme, fqdir, keyfile, kmerlen, h5)
|
shfile |
A shell script in "slurm-script/". [chr, "slurm-script/run_it.sh"] |
fqdir |
Absolute dir for the fastq files, can be nested within the dir. [chr, "my/fq/filedir"] |
keyfile |
The key file. The GBSv2 key file has 4 required headers: Flowcell, Lane, Barcode and FullSampleName. [chr, "data/file.txt] |
bt2_idx |
The idx file for bowtie2. [chr, "/lustre/work/jyanglab/jyang21/dbcenter/AGP/AGPv4/AGPv4_bt2_index/AGPv4_bt2_index"] |
sam |
The output sam file. [chr, "tagexport/tagsForAlignFullvs_F1s.sam"] |
ref |
Fastq file of the ref. [chr, "/lustre/work/jyanglab/jyang21/dbcenter/AGP/AGPv4/AGPv4_bt2_index/AGPv4_bt2.fa"] |
snpqc_file |
SNP qc file. [chr, "largedata/gbs/outputStats.txt"] |
h5 |
Output hdf5 format. [chr, "gbs/discovery/output.h5"] |
db |
Relative file name of the db. [chr, =NULL, or "data/gbs.db"] |
mem |
Memory usage. [num, 50] |
cpu |
Number of CPUs to use. [num, 50] |
kmerlen |
Kmer length [num, =64] |
enzyme |
Enzyme used for cutting. [chr, ="ApeKI"] |
mnlcov |
mnLCov. [num, =0.05] |
mnmaf |
Min MAF. [num, =0.001] |
deleteolddata |
Delete Old Data. [chr, ="true"] |
production |
SNP production. [logical, =F] |
seq2tag |
Generated tags from fastq files. [logical, =T] |
tag2fq |
extract tags from db for alignment to reference. [logical, =T] |
bt2 |
Run bt2 alignment. [logical, =T] |
snpcall |
Call SNP. [logical, =T] |
tagexport |
Fastq.gz file to export tags. [chr, "tagexport/tagsForAlign.fa.gz"] |
mindepth |
The minimum count of reads for a tag to be output. [num, =1] |
return a batch of shell scripts.
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