I'm trying to derive a vcf file from a bam using:
samtools view -bS test.sam | samtools sort - test_sort
samtools index test_sorted.bam
samtools mpileup -E -uf Ref.fna test_sorted.bam > test.pileup
bcftools view -cg test.pileup > test.vcf
The sam and bam look fine but the mpileup command runs too quickly and gives me a small file without sequence data.
bcftools gives me:
[bcf_sync] incorrect number of fields (6 != 5) at 0.0
I've re-generated the bowtie index with the Ref.fna file to confirm the files match but that doesn't help. I'm using samtools 1.2, bcftools 0.1.17.
Any idea what's wrong? It worked fine a couple of weeks ago.
samtools view -bS test.sam | samtools sort - test_sort
samtools index test_sorted.bam
samtools mpileup -E -uf Ref.fna test_sorted.bam > test.pileup
bcftools view -cg test.pileup > test.vcf
The sam and bam look fine but the mpileup command runs too quickly and gives me a small file without sequence data.
bcftools gives me:
[bcf_sync] incorrect number of fields (6 != 5) at 0.0
I've re-generated the bowtie index with the Ref.fna file to confirm the files match but that doesn't help. I'm using samtools 1.2, bcftools 0.1.17.
Any idea what's wrong? It worked fine a couple of weeks ago.
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