I could extract the unmapped reads from the bwa-mem alignment file in SAM format using below command
samtools view -S -f0x4 alnIRGSP.sam > UNMAP.sam.
After that i could not convert this sam file to bam file . I get the below error.
[bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "sortUNMAP.sam".
Can anyone help me to solve this..