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
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
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