I tried using BCFtools but I keep getting an error.
1. I had 2 SAM files that converted to BAM, sorted by chromosome, and finally indexed using Picard.
2. Using the 2 manipulated BAM files, I used the mpileup command in SAMtools. Here is the specific command:
samtools mpileup -f ref.fa in.bam in2.bam > in_in2_pileup.bcf
3. After this step I wanted to get the vcf format. I used bcftools and the command view in order to do this:
bcftools view in_in2_pileup.bcf > in_in2_pileup.vcf
The error that I received after executing this command:
incorrect number of fields (0 != 5) at 0:0
PS. I tried looking my problem up in google search and every example seemed to be irrelevant in my case.
1. I had 2 SAM files that converted to BAM, sorted by chromosome, and finally indexed using Picard.
2. Using the 2 manipulated BAM files, I used the mpileup command in SAMtools. Here is the specific command:
samtools mpileup -f ref.fa in.bam in2.bam > in_in2_pileup.bcf
3. After this step I wanted to get the vcf format. I used bcftools and the command view in order to do this:
bcftools view in_in2_pileup.bcf > in_in2_pileup.vcf
The error that I received after executing this command:
incorrect number of fields (0 != 5) at 0:0
PS. I tried looking my problem up in google search and every example seemed to be irrelevant in my case.
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