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  • Samtools mpileup error "[W::sam_read1] parse error at line 1"

    Hello everyone,

    I am analyzing WGS data of my mutant (Raw data in fastq), I performed the alignment by using Bowtie and BWA as:

    Using Bowtie:
    bowtie -S reference.fa file.sam
    then converted the sam file to bam file
    samtools view -bS -o file.bam file.sam

    Using BWA:
    bwa aln reference.fa file.fastq > file.sai
    bwa samse reference.fa file.sai file.fastq gzip > file.sam.gz

    then converted sam.gz to bam
    samtools view -bt reference.fa file.sam.gz | samtools sort -o file.bam

    Then I tried to use mpileup on both bam files but got similar errors:

    samtools mpileup -v reference.fa file.bam > outfile

    [mpileup] 2 samples in 2 input files
    <mpileup> Set max per-file depth to 4000
    [W::sam_read1] parse error at line 1

    Can anyone explain whats wrong and how it can be corrected?
    Thanks

  • #2
    Check samtools mpileup man page.
    You may want to try -f instead of -v ?

    Comment


    • #3
      Are you using the newest versions of bwa/samtools?

      Comment


      • #4
        @dschika will it then give vcf format output?

        @GenoMax,

        I am using bwa-0.7.13 and
        samtools-1.3

        Comment


        • #5
          Ok, probably you want to use -v and -f, my bad.

          As you read the manual which you can find here, you know what -v and -f do:

          -f, --fasta-ref FILE The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by bgzip.
          -v, --VCF Compute genotype likelihoods and output them in the variant call format (VCF). Output is bgzip-compressed VCF unless -u option is set.

          Comment

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