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What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
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Dear [Brian][1] I realized that problem is with callvariants.sh script because when I called variants using freebayes I did not find aforem…
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Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
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again, it's a problem with the variant caller, which is ?
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
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Not only opposite case but same case nucleotides are also present in vcf fle.
![enter image description here][1]
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Yes [Pierre][1] there is lower case **g** in **REF** and upper case **G** in **ALT** field. My question is that why variant caller is calli…
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This is an error in your input vcf file. The REF allele MUST be différent from the ALT allele.
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Do I need to convert lower case nucle…
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I observed that both lower and upper cases are present in reference fasta file. Is bbtool case sensitive that while calling variants it con…
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