/volume2/web/Atumefaciens/20210909-cbai-bcftools-snp_calling

SNP Identification - C.bairdi Day 2 DEG Pooled Samples Using bcftools on Mox

HISAT2 alignment of C.bairdi RNAseq to cbai_transcriptome_v3.1 transcriptome assembly
using HISAT2 index generated on 20210908. Followed by bcftools to identify SNPs in 
C.bairdi Day 2 DEG Pooled Samples.

- 20210909-cbai-bcftools-snp_calling.sh: SLURM script used to run job on Mox HPC.

- cbai_v3.1-SNPS.vcf: Variant Call Format file identifying SNPs.

- checksums.md5: MD5 checksums for all files in this directory.

- input_bam_checksums.md5: MD5 checksums for input BAM files used for SNP analysis. Also serves as a list
to document input BAM files used.

- program_options.log: Log of program options/help menus for programs used in SLURM script.

- slurm-2194047.out: Standard output captured by SLURM job.

- system_path.log: Log of all programs in Mox system $PATH at runtime.

Notebook:

https://robertslab.github.io/sams-notebook/2021/09/09/SNP-Identification-C.bairdi-Day-2-DEG-Pooled-Samples-Using-bcftools-on-Mox.html