Hi
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)
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
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,
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)
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
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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