Comments (17)
Sorry for late reply. If this is still relevant. Please supply files.
Thanks!
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Here you go: The files are too large to fit so I've attached a link to them in Dropbox: https://www.dropbox.com/sh/sle2vmlvc8jr6sb/AAD4vYwjyYn7Mo6xxDrYDtwia?dl=0
This is my input code:
#make glf and mafs files
echo "/work/07707/dgallery/ls6/software/angsd/angsd -b bams_kinship -gl 2 -domajorminor 1 -snp_pval 1e-6 -domaf 1 -minmaf 0.05 -doGlf 3 -out kinMAT" > kins
ls6_launcher_creator.py -j kins -n kins -t 2:00:00 -e $email -w 1 -a $allo
sbatch kins.slurm
#remove header from mafs
zcat kinMAT.mafs.gz | cut -f5 |sed 1d >freq
#make kinship matrix
echo "/work/07707/dgallery/ls6/software/ngsRelate/ngsRelate -g kinMAT.glf.gz -n 65 -f freq -O kinMAT" > kins2
ls6_launcher_creator.py -j kins2 -n kins2 -t 2:00:00 -e $email -w 1 -a $allo
sbatch kins2.slurm
Thank you for your help!
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Related Issues (20)
- No output
- Problem with guess in emStep: 0.350616 0.350616 ... (unrelated to previous posts) HOT 8
- nIter = -1? Actually bestoptimll = -1? HOT 4
- verbose output HOT 3
- rmTrans option HOT 1
- extract_freq_bim error HOT 4
- Interpretation of relatedness (rab) coefficient HOT 4
- PL field in VCF HOT 4
- Add a LICENSE file
- possible to convert beagle to binary beagle (doGlf 2 to doGlf 3) or use beagle file as input? HOT 3
- Coverage HOT 2
- unexpected high theta values HOT 2
- [Question] Merging ANGSD Outputs HOT 5
- How does NgsRelate handle "missing data?" HOT 3
- Problem with guess in emStep: -nan HOT 2
- Bad results starting from beagle files? HOT 5
- Interpreting the inbreeding only Output.
- autocorrelation? HOT 1
- Something wrong with freq HOT 1
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