When importing sam to bam, I use 'view' rather than 'import' :
@SQ header lines present in SAM file:
samtools view –bS alignment.sam > alignment.bam
@SQ header lines absent from SAM file:
samtools view –bt reference.fasta.fai alignment.sam > alignment.bam
Not sure if that will help at all but might be worth a try
Good luck
@SQ header lines present in SAM file:
samtools view –bS alignment.sam > alignment.bam
@SQ header lines absent from SAM file:
samtools view –bt reference.fasta.fai alignment.sam > alignment.bam
Not sure if that will help at all but might be worth a try
Good luck
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