update doc with BED isbps

docs/source/pipeline_conf.md

@@ -96,14 +96,19 @@ targetGmapIndexPath: '/data/db/triticum_aestivum/julius/current/gmapdb/all/'
 
 
 ##### ISBP/markers related config and parameters
-# BAM file of markers/ISBPs mapped on the target genome (REFSEQ v2.1)
-isbpBam: 'data/iwgsc_refseqv1_ISBP.bwav2.1.bam'
-# BED file of coordinates on the query genome (REFSEQ v1.0)
-isbpBed: 'data/ISBP_refseqv1.bed'
+# BAM file of markers/ISBPs mapped on the target genome
+# isbpBam: '/home/masirvent/wheat10plus-pangenome/data/mappingISBP/session2/arina/arina_CS_ISBP.bam'
+# BED file of coordinates on the query genome (REFSEQ v2.1)
+isbpBed: 'data/Tae.Chinese_Spring.refSeqv2.1.ISBPs.bed'
+# BWA threads for mapping
+bwaThreads: 16
+# FLAG : F flag for samtools
+flag_F: 3844
 # minimum mapping quality of markers on the target genome
 mapq: 30
 # max mismatches per ISBP/marker
-mismatches: 0
+mismatches: 2
+
 
 ##### OUTPUT directory
 results: 'resultsDEV'