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sangu

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sangu
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  • Hello, I get GT:DP ./.:0 for one block of non-variants in gvcf. However, there is enough number of reads for this block. I have another block of non-variants showing GT:DP 0/0:6. But the number of reads for both the blocks is almost similar and I…
  • Hi @bshifaw, Thanks! I have gone through the tutorial but I am still not sure if my files are correct. And I was missing 'call' command with samtools so it was generating a big file which did not have true variants.
  • Hello, So I figured out why the .vcf file with samtools is so large than the .vcf file with gatk. But before moving ahead, I still want to make sure vcf file from gatk is also correct. I read the documentation you mentioned earlier. I have compar…
  • I have uploaded the files. Unfortunately, I found to upload single archive file after I did my files. I hope it will be okay this time. My file names are: bamout.bam bowtie.bam.gz bowtie_gatk.vcf.gz
  • I will share the data. Is there no error in the command lines that I am using!
  • Here is one screenshot attached of the difference in SNPs found in gatk vs samtools