I aligned short reads by an nonpublished aligner. Then I converted the
alignments to sam, then bam, and sote bam. It looks they worked for
me. But, when I intend to index and mpileup bam of multiple samples to
call variant. I faced a problem, I got errors:
$ samtools index maplistbam-sorted.bam
[bam_header_read] EOF marker is absent.
[bam_index_core] truncated file? Continue anyway. (-2)
I did these analysis using SAMtools-0.1.6, and it is said that the
updated verison of SAMtools can add header when converting sam to bam.
So, now I updated SAMtools to SAMtools-0.1.12. And I want to reconvert
my sam to bam. But, I am not sure how to do that.
(1) Can I use this command:
samtools view -bht my.fa.fai my.sam > my.bam
(2) Do I need add other arguments in the command?
(3) Please also help me to check if my sam file is a good one.
I need your helps. Thanks in advance.
Jian-Feng
Following is my old bam header:
$ samtools view -H maplistbam-sorted.bam
[bam_header_read] EOF marker is absent.
@SQ SN:1 LN:33132539
@SQ SN:2 LN:19320864
@SQ SN:3 LN:24464547
@SQ SN - - - - - - - - - -
My sam looks like this:
110210010374503018 67 1 1 0 68M1D3M1I3M
* 0 0
TCACTTTCACTTCTGGATGCTTGTGGTTAAACACCTCACCATTCCTGTTCAACTCCTCCCCCTGTTTCGTTCCCG
CCCCCCCCCCCCCCCACCCCCCCDC##################################################
MD:Z:26A2T38^A3N1A1
110211181203212143 67 1 4 0 101M *
0 0
CTTTCACTTCTGGATGCTTGTGGATATACACCTCACCATTCCTGTTCAACTCCTCCCCCTGTTTCAGTTCAGCAAAAGTTTAACTCTGCGGACGGCATCTA
CCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCDCCCDDBBCBCC@DCBCDDCBBCDBB>@>ABBDDBDCBBBDBBBDCBABBBACAB>>B-8A?A?CAA:BB
MD:Z:101
110210940527208528 137 1 5 0 101M *
0 0
TTTCACTTCTGGATGCTTGTGGATATACACCTCACCATTCCTGTTCAACTCCTCCCCCTGTTTCAGTTCAGCAAAAGTTTAACTCTGCGGACGGCATCTAC
@@BBA@B=@ABBB=>@@B@B=BBBBBBBBBBBBBBBBB@BBB>@BBBBB@@@@BBB==:B<@B@@@-@@:>@@B@A@@9AABB@B:/2/?BABBA<4@/>B
MD:Z:101
110210850423407552 153 1 6 0 95M *
0 0
TGCCGTCCGCAGAGTTAAACTTTTGCTGAACTGAAACAGGGGGAGGAGTTGAACAGGAATGGTGAGGTGTATATCCACAAGCATCCAGAAGTGAA
CCCCCCCCCCCCCCCCCCCCCCCCCCC8CCCCCCACCCCCCACA@@:CBBACCCCCCBA<CB.@>:6(9(;@@:<B@BCDBDB@D@>B@9@0@6@
MD:Z:95
503410211145216346 153 1 6 0 101M *
0 0
GGTAGATGCCGTCCGCAGAGTTAAACTTTTGCTGAACTGAAACAGGGGGAGGAGTTGAACAGGAATGGTGAGGTCTATATCCACAAGCATCCAGAAGTGAA
<<9'<AAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD@@@CBCCACCCCC@<CCCABBCB9CBBBBBADAB@CBBB?AB;BA5?5<>:
MD:Z:26C74
503410941820117468 153 1 7 0 85M *
0 0
CATCAATACTCTTTTGCTGAACTGAAACAGGGGGAGGAGTTGAACAGGAATGGTGAGGTGTATATCCACAAGCATCCAGAAGTGA
CCCCCCCCCCCCCCCBCCCCCCCCCCCCC6CCCCBBB:CBCCCCCCCC?CCCC@C?BB*B+;<?
alignments to sam, then bam, and sote bam. It looks they worked for
me. But, when I intend to index and mpileup bam of multiple samples to
call variant. I faced a problem, I got errors:
$ samtools index maplistbam-sorted.bam
[bam_header_read] EOF marker is absent.
[bam_index_core] truncated file? Continue anyway. (-2)
I did these analysis using SAMtools-0.1.6, and it is said that the
updated verison of SAMtools can add header when converting sam to bam.
So, now I updated SAMtools to SAMtools-0.1.12. And I want to reconvert
my sam to bam. But, I am not sure how to do that.
(1) Can I use this command:
samtools view -bht my.fa.fai my.sam > my.bam
(2) Do I need add other arguments in the command?
(3) Please also help me to check if my sam file is a good one.
I need your helps. Thanks in advance.
Jian-Feng
Following is my old bam header:
$ samtools view -H maplistbam-sorted.bam
[bam_header_read] EOF marker is absent.
@SQ SN:1 LN:33132539
@SQ SN:2 LN:19320864
@SQ SN:3 LN:24464547
@SQ SN - - - - - - - - - -
My sam looks like this:
110210010374503018 67 1 1 0 68M1D3M1I3M
* 0 0
TCACTTTCACTTCTGGATGCTTGTGGTTAAACACCTCACCATTCCTGTTCAACTCCTCCCCCTGTTTCGTTCCCG
CCCCCCCCCCCCCCCACCCCCCCDC##################################################
MD:Z:26A2T38^A3N1A1
110211181203212143 67 1 4 0 101M *
0 0
CTTTCACTTCTGGATGCTTGTGGATATACACCTCACCATTCCTGTTCAACTCCTCCCCCTGTTTCAGTTCAGCAAAAGTTTAACTCTGCGGACGGCATCTA
CCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCDCCCDDBBCBCC@DCBCDDCBBCDBB>@>ABBDDBDCBBBDBBBDCBABBBACAB>>B-8A?A?CAA:BB
MD:Z:101
110210940527208528 137 1 5 0 101M *
0 0
TTTCACTTCTGGATGCTTGTGGATATACACCTCACCATTCCTGTTCAACTCCTCCCCCTGTTTCAGTTCAGCAAAAGTTTAACTCTGCGGACGGCATCTAC
@@BBA@B=@ABBB=>@@B@B=BBBBBBBBBBBBBBBBB@BBB>@BBBBB@@@@BBB==:B<@B@@@-@@:>@@B@A@@9AABB@B:/2/?BABBA<4@/>B
MD:Z:101
110210850423407552 153 1 6 0 95M *
0 0
TGCCGTCCGCAGAGTTAAACTTTTGCTGAACTGAAACAGGGGGAGGAGTTGAACAGGAATGGTGAGGTGTATATCCACAAGCATCCAGAAGTGAA
CCCCCCCCCCCCCCCCCCCCCCCCCCC8CCCCCCACCCCCCACA@@:CBBACCCCCCBA<CB.@>:6(9(;@@:<B@BCDBDB@D@>B@9@0@6@
MD:Z:95
503410211145216346 153 1 6 0 101M *
0 0
GGTAGATGCCGTCCGCAGAGTTAAACTTTTGCTGAACTGAAACAGGGGGAGGAGTTGAACAGGAATGGTGAGGTCTATATCCACAAGCATCCAGAAGTGAA
<<9'<AAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD@@@CBCCACCCCC@<CCCABBCB9CBBBBBADAB@CBBB?AB;BA5?5<>:
MD:Z:26C74
503410941820117468 153 1 7 0 85M *
0 0
CATCAATACTCTTTTGCTGAACTGAAACAGGGGGAGGAGTTGAACAGGAATGGTGAGGTGTATATCCACAAGCATCCAGAAGTGA
CCCCCCCCCCCCCCCBCCCCCCCCCCCCC6CCCCBBB:CBCCCCCCCC?CCCC@C?BB*B+;<?
Comment