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John Marshall
John Marshall
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samtools sort -n file -o{file}_sorted.bam

This is essentially a duplicate of Samtools Index: Chromosome Blocks not Continuous but with different error messages, and a duplicate of Error given while trying to index a BAM file with Samtools Index - NO COOR?.

samtools sort -n ${file} -o ${file}_sorted.bam

These error messages also indicate that the reads are not sorted by coordinate — in particular, that the unplaced unmapped reads with RNAME * are not all together at the end of the file.

This is because samtools sort -n has been used to sort the reads by name instead. Remove -n to sort by position, which is what is needed to prepare a BAM file for indexing with samtools index.

samtools sort -n file -o{file}_sorted.bam

This is essentially a duplicate of Samtools Index: Chromosome Blocks not Continuous but with different error messages.

These error messages also indicate that the reads are not sorted by coordinate — in particular, that the unplaced unmapped reads with RNAME * are not all together at the end of the file.

This is because samtools sort -n has been used to sort the reads by name instead. Remove -n to sort by position, which is what is needed to prepare a BAM file for indexing with samtools index.

This is essentially a duplicate of Samtools Index: Chromosome Blocks not Continuous but with different error messages, and a duplicate of Error given while trying to index a BAM file with Samtools Index - NO COOR?.

samtools sort -n ${file} -o ${file}_sorted.bam

These error messages also indicate that the reads are not sorted by coordinate — in particular, that the unplaced unmapped reads with RNAME * are not all together at the end of the file.

This is because samtools sort -n has been used to sort the reads by name instead. Remove -n to sort by position, which is what is needed to prepare a BAM file for indexing with samtools index.

Source Link
John Marshall
John Marshall
  • 1.1k
  • 8
  • 12

samtools sort -n file -o{file}_sorted.bam

This is essentially a duplicate of Samtools Index: Chromosome Blocks not Continuous but with different error messages.

These error messages also indicate that the reads are not sorted by coordinate — in particular, that the unplaced unmapped reads with RNAME * are not all together at the end of the file.

This is because samtools sort -n has been used to sort the reads by name instead. Remove -n to sort by position, which is what is needed to prepare a BAM file for indexing with samtools index.