MegaMapper is comprised of two pipelines developed by the Megason Lab at Harvard University. The pipelines are HMFseq and BSFseq.
The following instructions detail how to run MegaMapper on TACC from the command line. This is a DRAFT version. This pipeline has not been fully validated. Some of the scripts have file references hard-coded in the source. The pipeline will be refined as demand dictates.
Sample
, so just run
mkdir Sample |
fastExon-mpileup Sample_R1.fastq Sample_R2.fastq 8000000 3 |
cat Test.snps.vcf | java -jar /work/01863/benni/snpEff_3_1/SnpSift.jar filter "( DP > 2 ) & ( DP < 32 ) & ( QUAL >= 10 ) ! (REF = 'N') ! (ALT = 'N')" > mapping_clean_snps.vcf |
module load java64 cat Test.snps.vcf | java -Xmx6G -jar /work/01863/benni/snpEff_3_1/SnpSift.jar filter "( DP > 2 ) & ( DP < 32 ) & ( QUAL >= 10 ) ! (REF = 'N') ! (ALT = 'N')" > mapping_clean_snps.vcf |
cat variants.snps.vcf | java -Xmx6G -jar /work/01863/benni/snpEff_3_1/SnpSift.jar filter "( DP > 5 ) & ( DP < 32 ) & ( QUAL >= 10 ) & (DP4[2] > 0) & (DP4[3] > 0) ! (REF = 'N') ! (ALT = 'N')" > mapping_snps.vcf |
sed '1,27d' mapping_snps.vcf > mapping_snps_headless.vcf |
python covextract.py -f mapping_snps_headless.vcf > mapping_snps.tab |
gawk -F=$'\t' 'sub(/variants.*bcf:/, "", $1)' mapping_snps.tab > mapping_snps_nums.tab |
Rscript --vanilla /corral-repl/utexas/BioITeam/bin/MegaMapper/HMFseq_Rscript mapping_snps_nums.tab HMFseq_output.tab HMFseq_genome_plot.pdf HMFseq_chromosome_scan.pdf "<Run_Name>" |
<Run_Name>
is whatever you want to call this run.)java -jar /work/01863/benni/snpEff_3_1/snpEff.jar eff -c /work/01863/benni/snpEff_3_1/snpEff.config -i vcf -o txt -upDownStreamLen 10000 -hom -no None,downstream,intergenic,intron,upstream,utr -stats all_SNPeff_output.tab Zv9.68 clean_snps_nums.vcf > snpEff_output.txt |
module load bedtools |
intersectBed -v -a clean_snps_nums.vcf -b ../dbSNP/vcf_chr_1-25.vcf > remaining_snps1.vcf intersectBed -v -a remaining_snps1.vcf -b WT_SNP_set.vcf > remaining_snps2.vcf |
python /corral-repl/utexas/BioITeam/bin/MegaMapper/VCFheader_mod.py remaining_snps3.vcf remaining_snps2.vcf |
java -jar /corral-repl/utexas/BioITeam/bin/snpEff_3_1/snpEff.jar eff -c /corral-repl/utexas/BioITeam/bin/snpEff_3_1/snpEff.config -i vcf -o txt -upDownStreamLen 5000 -hom -no None,downstream,intergenic,intron,upstream,utr -stats unfiltered_stats.tab Zv9.68 remaining_snps3.vcf > unfiltered_candidate_SNPs.tab |
Rscript --vanilla /corral-repl/utexas/BioITeam/bin/MegaMapper/candidator.R unfiltered_candidate_SNPs.tab HMFseq_output.tab candidate_list.tab |
candidate_list.tab
file is your output. Congratulations, you're done!