Hi,
Can someone explain the following phenomenon. I ran bcftools (bcftools call -v -c )on a pileup created by samtools. This resulted in calling of a SNP. Next I extracted reads spanning the SNP, created the pileup and ran bcftools as before. I was expecting that bcftools would give me back the same result but was surprised when no SNP was predicted. Why does this happen?
Can someone explain the following phenomenon. I ran bcftools (bcftools call -v -c )on a pileup created by samtools. This resulted in calling of a SNP. Next I extracted reads spanning the SNP, created the pileup and ran bcftools as before. I was expecting that bcftools would give me back the same result but was surprised when no SNP was predicted. Why does this happen?
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