jinzhuangdou
commented
5 years ago Hi, you vcf file does not have the dosage information. You should use the -GT mode to take the genotype.
Open vinay-swamy opened 6 years ago
jinzhuangdou
commented
5 years ago Hi, you vcf file does not have the dosage information. You should use the -GT mode to take the genotype.
Hi there, I was attempting to run seekin using the following command, using a vcf I generated with vcf-merge I made sure the resulting file was then converted to gzip format, and ran seekin ./seekin kinship -i $space/test1.vcf.gz -r 0.3 -m 0.05 -d DS -p hom -l 2000 -t 1 -w 1 -o test This is the output: SEEKIN: SEquence-based Estimation of kinship Version 1.01: released on 2017-Oct-10
Module kinship
Parameters: -i /home/vinayswamy/Documents/PROJECTS/aldave_lab/wex/variant_samples/test1.vcf.gz -f [] -o test -r 0.300000 -m 0.050000 -d DS -p hom -s 0 -w 1 -l 2000 -t 1
[Fri Jul 13 11:55:19 2018] Started! [Fri Jul 13 11:55:19 2018] No individual-specific allele frequency file is specified! [Fri Jul 13 11:55:19 2018] Use the hom mode with weight function 2MAF(1-MAF)Rsq^2 [Fri Jul 13 11:55:19 2018] BLOCK_SIZE is set to 2000 [Fri Jul 13 11:55:19 2018] THREAD_NUM is set to 1 [Fri Jul 13 11:55:19 2018] MAF filter 0.05 [Fri Jul 13 11:55:19 2018] R2 filter 0.3 [Fri Jul 13 11:55:19 2018] GENOTYPE MODE DS [Fri Jul 13 11:55:19 2018] Reading the markers in /home/vinayswamy/Documents/PROJECTS/aldave_lab/wex/variant_samples/test1.vcf.gz Segmentation fault (core dumped)
I also ran the same command, but used the -s 1 argument for small sample sizes
SEEKIN: SEquence-based Estimation of kinship Version 1.01: released on 2017-Oct-10
Module kinship
Parameters: -i /home/vinayswamy/Documents/PROJECTS/aldave_lab/wex/variant_samples/test1.vcf.gz -f [] -o test. -r 0.300000 -m 0.050000 -d DS -p hom -s 1 -w 1 -l 2000 -t 1
[Fri Jul 13 12:01:49 2018] Started! [Fri Jul 13 12:01:49 2018] No individual-specific allele frequency file is specified! [Fri Jul 13 12:01:49 2018] Use the hom mode with weight function 2MAF(1-MAF)Rsq^2 [Fri Jul 13 12:01:49 2018] Start the algorithm model for small sample size, make sure that the individual-specific allele frequency file exists [Fri Jul 13 12:01:49 2018] BLOCK_SIZE is set to 2000 [Fri Jul 13 12:01:49 2018] THREAD_NUM is set to 1 [Fri Jul 13 12:01:49 2018] MAF filter 0.05 [Fri Jul 13 12:01:49 2018] R2 filter 0.3 [Fri Jul 13 12:01:49 2018] GENOTYPE MODE DS [Fri Jul 13 12:01:49 2018] Start the algorithm model for small sample size terminate called after throwing an instance of 'std::runtime_error' what(): FAIL_IO: Failed to Open [] for r Aborted (core dumped)
I've attatched the file I used as well. Let me know If there's anything I'm doing wrong, or if there is a fix. Thank You
test1.vcf.gz