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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| IntroMap_v1.tar.gz | 2016-07-29 | 70.7 MB | |
| README | 2016-07-29 | 6.8 kB | |
| Totals: 2 Items | 70.7 MB | 0 |
Automated pipeline for mapping alien introgressions with Next Generation Sequence data ################################################################################################################## # # # # REQUIRED: # # -b <string> sorted/indexed bam file of alignments # # -g <string> indexed genome # -df <string> diploid species diagnostic SNP positions file # -bf <string> diploid species alternate bases file # -o <string> filtered vcf output name # # OPTIONAL: # --no_cleanup does not delete intermediate vcf files: default (FALSE) # # OPTIONAL PIPELINE TO FIND NEW DIAGNOSTIC SNPS FIRST. PRECEDING PARAMTERS ARE REQUIRED WITH THIS OPTION # --find_dagnostic turns option pipeline on: default (FALSE) # -d <string> sorted/indexed bam file of diagnostic accession/species alignment # -c <string> sorted/indexed bam file of control accessions/species alignments # Use as many as available. The more used, the more confidence gained in diagnostic set # -pre <string> Prefix for new SNP sets. Will be placed in basefiles directory # PLEASE ALSO SHARE WITH DEVELOPER TO BE INCLUDED IN SUBSEQUENT RELEASES # When sharing please include accession, genus, species, PI #, etc # ################################################################################################################ # # To use this script there are certain requirements: # # (1) Samtools v0.1.9 and Bcftools v0.1.9 must be in your path -> Will not work with later versions (can be downloaded at # https://sourceforge.net/projects/samtools/files/samtools/0.1.9/ # (2) To do this easily you can add the path in your shell script # (3) alignment Bam files must be sorted and indexed # (5) Example command line: # # perl IntroMap.pl -b gen.sorted.bam -g genome.fa -bf car.bases -df car.list -o output.txt # # or to find new diagnostic SNPs: # # perl IntroMap.pl -b gen.sorted.bam -g genome.fa -o output.txt --find_diagnostic -d newspecies.sorted.bam\ # -c control1.sorted.bam -c control2.sorted.bam -pre new # ################################################################################################################# Included diagnostic SNP sets with current release: Arachis cardenasii accession GKP10017 PI 26214: filenames for use: car.list,car.bases Arachis diogoi accession GKP10602 PI 276235: filenames for use: dig.list,dig.bases Arachis stenosperma accession V10309 PI 666100: filenames for use: sten.list,sten.bases Arachis magna accession KG30097 PI 468340: filenames for use: mag.list,mag.bases Arachis batizocoi accession K9484 PI 298639: filenames for use: bat.list,bat.bases