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

[znasim09]

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

[dschika]

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

[GenoMax]

Are you using the newest versions of bwa/samtools?

[znasim09]

@dschika will it then give vcf format output?

@GenoMax,

I am using bwa-0.7.13 and
samtools-1.3

[dschika]

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.