Question: Reference genome and samtools reheader option
gravatar for shuksi1984
12 months ago by
shuksi198450 wrote:

With respect to the reference sequence hg38 and gatkbundlehg38, I used gatkbundlehg38 and hg38.fa for alignment of exome sequence. I am getting error while using samtools reheader.

my command is: path/to/samtools reheader -i HG100.sam > HG100.bam

I got following error both the times.

[E::hts_open] fail to open file '-i' [main_reheader] fail to read the header from -i.

HG100.sam is 4.9GB

Following shows it's header details:

@SQ SN:chr1 LN:248956422
@SQ SN:chr2 LN:242193529
@SQ SN:chr3 LN:198295559
@SQ SN:chr4 LN:190214555
@SQ SN:chr5 LN:181538259
@SQ SN:chr6 LN:170805979
@SQ SN:chr7 LN:159345973
@SQ SN:chr8 LN:145138636
@SQ SN:chr9 LN:138394717
@SQ SN:chr10 LN:133797422
ADD COMMENTlink modified 12 months ago • written 12 months ago by shuksi198450

Can you clear, from where you are getting "your_alignments.bam" in second command. We get BAM file only when we convert SAM to BAM after alignment with reference genome. I have just aligned my exome data with the reference genome, hence do not have any BAM file.

This is my actual command: sudo path/to/samtools-1.2/bin samtools reheader -i HG100.aligned_reads.sam > HG100_aligned_reads_reheader.bam

samtool version is 1.2

ADD REPLYlink written 12 months ago by shuksi198450

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

This comment belongs under @Devon's answer.

A side note. Running user programs should never need sudo.

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax65k

Most people don't ever produce SAM files, they invoke samtools view to produce BAM files directly. You can probably use a SAM file as input into samtools reheader, though since it's already a text file that one can directly edit I've never tried.

ADD REPLYlink written 12 months ago by Devon Ryan89k

BTW, the -i option was added to samtools reheader in version 1.3.

ADD REPLYlink written 12 months ago by Devon Ryan89k
gravatar for Devon Ryan
12 months ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

The version of samtools you're using apparently doesn't support the -i option. Also, your command is wrong, it should be samtools reheader -i some_header_file_or_sam_file your_alignments.bam or samtools reheader some_header_file_or_sam_file your_alignments.bam > alignments_with_new_header.bam.

ADD COMMENTlink written 12 months ago by Devon Ryan89k
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