example.blastid.input

#example input file for bam2blastid.sh (1 June 2013)

#input bams
pathbams=/PATH/TO/BAMS				#path to realigned bams
bamsuffix=.markdup.realign.fixed.reorder.bam	#suffix for bam files

#sample ids (prefix for input bam files)
ids=( sampleA sampleB sampleC )

#initial species id for each sample
pre_taxa_id=( speciesA speciesB speciesC )

#minimum e-value to report blast hits
eval=0.001

#blast db
db_path=/PATH/TO/BLAST/DB		#path to blast db
db_file=blast.db.fa			#blast db fasta file
db_type=nucleotide			#type of blast database (protein or nucleotide)

#type of blast search (eg blastn, blastp, blastx, tblastn, tblastx) 
blast_type=blastn

#genomic region of interest
contig="contig_name"		#contig in reference with blast piece
start=100			#start position of blast piece
end=200				#end position of blast piece

#reference that was used for alignments
reference=/PATH/TO/REF/reference.fasta

#paths to programs
picard=/PATH/TO/PICARD/picard-tools-1.53
gatk=/PATH/TO/GATK/GenomeAnalysisTK-1.2-4-gd9ea764/GenomeAnalysisTK.jar

#number of threads to use
threads=10

#GATK genootyping variables
call_conf=30
emit_conf=10
mincov=10
maxcov=251	#GATK defaults to downsample every site to <251, so setting to 251 keeps everything
het=0.025
gqual=30.0

#email adress for notification when script completes
email2=name@domain.com