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How to get the qc_snp for chip imputation #1

Open baishengjun opened 2 years ago

baishengjun commented 2 years ago

Hi,

What a fantastic job! but I was confused with the qc_snp file. How to get it, and what will be the file format? Bai

scbaca commented 2 years ago

Thanks! The qc_snp file has locations of SNPs to select from for the rule "genotype_from_bam". It has to be formatted consistently with the -R argument for bcftools mpileup. Here's the head of the one I used:

chr11 193194 chr11 193863 chr11 196944

baishengjun commented 2 years ago

Hi, Thanks for your kind reply. I got ready the input file for the chip imputation pipeline but encountered a new problem. The following is the error log, the error message was short, and how to solve it to continue the pipeline. 124 of 578 steps (21%) done [Mon Sep 19 09:31:09 2022] Finished job 571. 125 of 578 steps (22%) done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/zhaoying/cuttag/BAMfiles/chipimputation/.snakemake/log/2022-09-18T194755.123342.snakemake.log

scbaca commented 2 years ago

There should be more info in the error message from the job that failed. Are you able to share it?