Hello,

I have a genome with homologous pairs of chromosome. I am using hisat2 to map RNA-seq reads to genome. I want to do variant calling with GATK, but before I want to extract the reads that mapped uniquely from BAM file(not SAM). Could you suggest how to do that? From other threads seems that flag NH:i:1 means mapped once, but how can I grep it from bam file? and is it a right way?

HISEQ1:128:C0HUMACXX:6:2210:15441:67674 163 chr1A   1101543 60  59M =   1104438 626 CAATCTTCTCGTGGTTTATTGGCGAATGGAGTTTCAGAAGATGCTCAAAATGGTTTCCA @BCFFDDEFHDDFGEEEDHEHCBHFD<3D3C*?D:B?:B?B*98D?4?BB=CG)=FFHA AS:i:0  ZS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:59 YS:i:0  YT:Z:CP NH:i:1
HISEQ1:130:C0G55ACXX:1:1203:2254:30173  163 chr1A   1101543 60  101M    =   1101599 155 CAATCTTCTCGTGGTTTATTGGCGAATGGAGTTTCAGAAGATGCTCAAAATGGTTTCCATGATGCTGATCGAACTGTCCGCAGAGGTGAGGGGCCATCTAA   CCCFFFFFHHHHHJGIJJJJJJJJJJJJJGIJIJJIJIJJJJJJJJJJJJJJJIIJJJJJJJJJJJJHHHHHFFFFEEEDDDDDDD@BDDDDDDDDDDDDD   AS:i:0  ZS:i:-15    XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:101    YS:i:-2 YT:Z:CP NH:i:1