why there are no nucleotides in the position of the reference genome after the SAMtools Mpileup

Posted in API by Ekaterina Mon Oct 15 2018 07:27:42 GMT+0000 (UTC)·2·Viewed 41 times

H! I have been creating workflow which consists three main steps ( SAMtools View, SAMtools fadix and SAMtools Mpileup). Firstly, with the SAMtools View I filtered the input bam-file based on a bed-file that contains special regions of the third and fifteenth chromosomes. The input bam-file already aligned and sorted I took from the database. The bed-file was download from my computer and the firs line looks like this (3 193593144 193697811). After that the SAMtools Mpileup took file that contain only necessary chromosomes and the file with the indexed reference (as a reference, I used ucsc.hg19.fasta from the database). At the end of the workflow, I expect to see vcf-file with that contains information about the reference and alternative nucleotide of the third and fifteenth chromosomes. Unfortunately, I get the described file, but there are N in place of the reference allele. Please help me understand what is wrong with my reference file
Manisha Ray
Oct 19, 2018

Hi Ekaterina,

Sorry you're running into this issue! To help us figure it out, can you email the link to the failed task in the project to support@sbgenomics.com? We'll look into from there.

Thanks!
Manisha

Manisha Ray
Oct 19, 2018

Hi Ekaterina,

Sorry you're running into this issue! To help us figure it out, can you email the link to the failed task in the project to support@sbgenomics.com? We'll look into from there.

Thanks!
Manisha

  
Markdown is allowed