Error Using Samtools To View Content In .Sam File

Question

[soosus]

So I'm working with a .SAM file that looks a little like this:

~$ zcat myfile.sam.gz | head -n5

@HD    VN:1.0    SO:coordinate
@RG    ID:PI    SM:PI-887    
@PG    ID:SOLID-GffToSam    VN:1.2.1
61_1240_1410    105    chr1    453    255    37M    *    0    0    CCCTAACCCTAACCCTCGCGGTACCCTCAGCCGGCCC    IIIIIIIIIIIIIIIIIIIIIIHG<II%%IID-;9EI    RG:Z:PI    CS:Z:T20023010023010022333013100222230303001200332030122    CO:i:0    CQ:Z:;B>@<>A=;>?@<74A@3>:6B362+B4%A:>''5%A,%1->%2/)>'3=    MD:Z:37M    NM:i:0
891_487_1977    115    chr1    49291    255    47M    =    52033    2792    TGCAGTGACAATATACATAAACAGTGTATGAAAACTCAAGTAAAATC    5II0/FIEB22IIIIFIII@GIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:PI    CS:Z:T12300031201221000213311121100331133331112111131101    CO:i:0    CQ:Z:<A?3>?A:4?:@=8<;>=4@?@64<<801@@9.?>>=26-98/0;<1%'8    MD:Z:47M    NM:i:0

and want to print reads that mapped in opposite orientation to the reference strand using this:

~$ samtools view -f 0x10 myfile.sam.gz

but I keep getting an error that looks like this:

[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from "solid0388_20100319_1_887_Paired_8.mates.sortedFragments.sam.gz".

Any suggestions? For what it's worth, I'm using the latest version of samtools in Fedora.

Answer 1

[Pierre Lindenbaum]

your input is SAM , not BAM

use

 gunzip -c myfile.sam.gz | samtools view -S -f 0x10 -T reference.fa -

[soosus]

I'm getting this:

[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

[Pierre Lindenbaum]

I've updated my answer.

[soosus]

Thanks very much!