Hi

I am trying to sort my bam file using samtools 0.1.19-44428cd

with the following command:

gives:

The bam file was generated in samtools with :

and the header in the sam file (generated with bwa) is

I also tried:

but got the same error.

I am just starting out in this area, and any help would be appreciated.

Thanks,

I am trying to sort my bam file using samtools 0.1.19-44428cd

with the following command:

**samtools sort test_sequence.bam test_sorted**gives:

*[bam_header_read] invalid BAM binary header (this is not a BAM file).*

Segmentation fault (core dumped)Segmentation fault (core dumped)

The bam file was generated in samtools with :

**samtools view -bS test_sequence.sam > test_sequence.bam**and the header in the sam file (generated with bwa) is

*@SQ SN:chr10 LN:135534747*

@SQ SN:chr11 LN:135006516

@SQ SN:chr11_gl000202_random LN:40103

@SQ SN:chr12 LN:133851895

@SQ SN:chr13 LN:115169878

@SQ SN:chr14 LN:107349540

@SQ SN:chr15 LN:102531392

@SQ SN:chr16 LN:90354753

@SQ SN:chr17_ctg5_hap1 LN:1680828

@SQ SN:chr17 LN:81195210@SQ SN:chr11 LN:135006516

@SQ SN:chr11_gl000202_random LN:40103

@SQ SN:chr12 LN:133851895

@SQ SN:chr13 LN:115169878

@SQ SN:chr14 LN:107349540

@SQ SN:chr15 LN:102531392

@SQ SN:chr16 LN:90354753

@SQ SN:chr17_ctg5_hap1 LN:1680828

@SQ SN:chr17 LN:81195210

I also tried:

**samtools view -bT wg.fa test_sequence.sam > test_sequence.bam**but got the same error.

I am just starting out in this area, and any help would be appreciated.

Thanks,

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