Hey everyone, I encountered this error when I tried to covert SAM file to BAM file. It looked like there was something wrong with my sam file. As it pointed out at a certain line there was a parse error.
The command I used to generate sam file was 'bwa mem -t 21 test2k.fa step3_SMPC-1_R1_shortReadRemoved.fq step3_SMPC-1_R2_shortReadRemoved.fq > test2k_aln-pe.sam' , then I tried 'samtools view -bT test2k.fa test2k_aln-pe.sam | samtools sort - test2k' and 'samtools view -Sb test2k_aln-pe.sam | samtools sort - test2k_aln-pe' but all failed due to that error. Is there anyway to re-generate the sam file? Thanks Kind regards. Fang ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
