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
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.
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
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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
Please use
ADD COMMENT/ADD REPLYwhen 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.Most people don't ever produce SAM files, they invoke
samtools viewto produce BAM files directly. You can probably use a SAM file as input intosamtools reheader, though since it's already a text file that one can directly edit I've never tried.BTW, the
-ioption was added tosamtools reheaderin version 1.3.