Reference genome and samtools reheader option

Question

[shuksi1984]

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

[shuksi1984]

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

[GenoMax]

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.

[Devon Ryan]

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.

[Devon Ryan]

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

Answer 1

[Devon Ryan]

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.

[lakhujanivijay]

This command does not perform replacement within the same bam file rather is spitting binary in std out. Any suggestion?

samtools reheader -i some_header_file_or_sam_file your_alignments.bam