hi all,
when I use samtools to get bam file from sam file? I met the following problems:
samtools view -h -F 4 -q 1 -bS C.filsa.sam >C.filsa.bam
[samopen] SAM header is present: 7 sequences.
[sam_read1] reference 'SR' is recognized as '*'.
[main_samview] truncated file.
I also met "missing colon in auxiliary data " and "CIGAR and sequence length are inconsistent" in individual rows. My sam files came from the results of gsnap. I am not sure these problem caused by gsnap or samtools. how can i deal with them?
Any suggestions and answers are appreciated. thank you.
when I use samtools to get bam file from sam file? I met the following problems:
samtools view -h -F 4 -q 1 -bS C.filsa.sam >C.filsa.bam
[samopen] SAM header is present: 7 sequences.
[sam_read1] reference 'SR' is recognized as '*'.
[main_samview] truncated file.
I also met "missing colon in auxiliary data " and "CIGAR and sequence length are inconsistent" in individual rows. My sam files came from the results of gsnap. I am not sure these problem caused by gsnap or samtools. how can i deal with them?
Any suggestions and answers are appreciated. thank you.
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