Post date: May 19, 2019 5:41:2 PM
Because I want to match the CHC genetic data with the timeseries analyses, I am recalling variants with samtools/bcftools. I made a new directory for this: /uufs/chpc.utah.edu/common/home/u6000989/data/lycaeides/lycaeides_chcs/Variants_timeseries
I ran sbatch SamVarCall.sh
which runs
#!/bin/sh
#SBATCH --time=240:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=24
#SBATCH --account=gompert-kp
#SBATCH --partition=gompert-kp
#SBATCH --job-name=sam_varcall
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=zach.gompert@usu.edu
#SAMTOOLs mpileup version 1.5 options used:
#C = adjust mapping quality; recommended:50, disable:0 [0]
#d = max per-file depth; avoids excessive memory usage [250]
#f = faidx indexed reference sequence file
#q = skip alignments with mapQ smaller than INT [0]
#Q = skip bases with baseQ/BAQ smaller than INT [13]
#g = generate genotype likelihoods in BCF format
#t = --output-tags LIST optional tags to output:DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR []
#BCFTOOLs call version 1.6 options used
#v = output variant sites only
#c/m = he original calling method (conflicts with -m) or alternative model for multiallelic and rare-variant calling (conflicts with -c)
#p = variant if P(ref|D)<FLOAT with -c [0.5]
#P = --prior <float-o mutation rate (use bigger for greater sensitivity), use with -m [1.1e-3]
#O = output type: 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' (here it is 'v')
#o = write output to a file [standard output]
module load samtools
module load bcftools
cd /uufs/chpc.utah.edu/common/home/u6000989/data/lycaeides/lycaeides_chcs/Variants_timeseries
samtools mpileup -C 50 -d 250 -f melissa_blue_21Nov2017_GLtS4.fasta -q 30 -Q 20 -g -I -t DP,AD -u -b bams.txt -o lyc_chcs_samtbcft.bcf
bcftools call -v -c -p 0.01 -P 0.001 -O v -o lyc_chcs_samtbcft.vcf lyc_chcs_samtbcft.bcf
I can then subset this (or not) to the SNPs used for the timeseries analysis.