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SEQLinkage

a collapsed haplotype pattern (CHP) method to generate markers from sequence data for linkage analysis

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SEQLinkage On Helix
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This example uses test data for a basic SEQLinkage run (User input in bold.)

[user@helix ~]$ mkdir /data/$USER/seqlinkage-example

[user@helix ~]$ cd /data/$USER/seqlinkage-example

[user@helix ~]$ module load seqlinkage
[+] Loading seqlinkage 1.0 on felix.nimh.nih.gov
[+] Loading singularity 2.2 on felix.nimh.nih.gov

[user@helix ~]$ cp $SEQLINKAGE_HOME/example-data/seqlinkage-example* .

[user@helix ~]$ seqlink --fam seqlinkage-example.fam --vcf seqlinkage-example.vcf.gz -f MERLIN
MESSAGE: Binary trait detected in [/spin1/users/godlovedc/seqlinkage-example/seqlinkage-example.fam]
MESSAGE: Checking local resources 5/5 ...
MESSAGE: 12 samples found in [/spin1/users/godlovedc/seqlinkage-example/seqlinkage-example.vcf.gz]
MESSAGE: 2 families with a total of 12 samples will be scanned for 25,305 pre-defined units
MESSAGE: 2 units (from 18 variants) processed; 3 Mendelian inconsistencies and 2 recombination events handled
MESSAGE: 25,302 units ignored due to absence in VCF file
MESSAGE: 1 units ignored due to absence of variation in samples
MESSAGE: Archiving regional marker data to directory [/spin1/users/godlovedc/seqlinkage-example/cache]
MESSAGE: 2 units will be converted to MERLIN format
MESSAGE: 2 units successfully converted to MERLIN format
MESSAGE: Archiving MERLIN format to directory [/spin1/users/godlovedc/seqlinkage-example/cache]
MESSAGE: Saving data to [/spin1/users/godlovedc/seqlinkage-example/LINKAGE]

[user@helix ~]$ ls -l LINKAGE/MERLIN/
total 16
-rw-r--r-- 1 godlovedc staff  17 Jan 13 14:54 LINKAGE.chr1.dat
-rw-r--r-- 1 godlovedc staff 109 Jan 13 14:54 LINKAGE.chr1.map
-rw-r--r-- 1 godlovedc staff 256 Jan 13 14:54 LINKAGE.chr1.ped
-rw-r--r-- 1 godlovedc staff  28 Jan 13 14:54 LINKAGE.chr16.dat
-rw-r--r-- 1 godlovedc staff 164 Jan 13 14:54 LINKAGE.chr16.map
-rw-r--r-- 1 godlovedc staff 304 Jan 13 14:54 LINKAGE.chr16.ped

Running a single SEQLinkage job on Biowulf
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Set up a batch script along the following lines:

#!/bin/bash
# file called myjob.bat

module load seqlinkage 
seqlink --fam foo.fam --vcf bar.vcf.gz -f MERLIN

Submit this job with:

[user@biowulf ~]$ sbatch myjob.bat

For more information on submitting jobs to slurm, see Job Submission in the Biowulf User Guide.

Running a swarm of SEQLinkage jobs on Biowulf
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Create a swarm command file like this sample

# --------file myjobs.swarm----------
seqlink --fam foo1.fam --vcf bar1.vcf.gz -f MERLIN
seqlink --fam foo2.fam --vcf bar2.vcf.gz -f MERLIN
seqlink --fam foo3.fam --vcf bar3.vcf.gz -f MERLIN
....
seqlink --fam fooN.fam --vcf barN.vcf.gz -f MERLIN
# -----------------------------------

Submit this set of runs to the batch system by typing

[user@biowulf ~]$ swarm --module seqlinkage -f myjobs.swarm

For details on using swarm see Swarm on Biowulf.

Documentation
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