Hi,
I'm encountering an issue with multiple gVCF files, all of which contain "N"-nucleotides in the REF column. In an attempt to resolve this, I used the fill-from-fasta plugin-function from bcftools with the following command:
bcftools +fill-from-fasta input_vcf.g.vcf.gz -- -c REF -f path/to/fasta_file/Homo_sapiens_assembly38.fasta
GATK was used to generate the gvcf-files. Thats why I downloaded and used the fasta-file from the GATK-github-repository.
I generated the gVCF files using GATK, and I downloaded the fasta file from the GATK GitHub repository.
However, the problem persists, and the "N"-nucleotides remain in the REF column.
bcftools query -f '[%CHROM\t%POS\t%REF\t%ALT\n]' inputvcf.g.vcf.gz|grep -v -E '[ACTG]' | head -n 10
Is there something wrong with my code, the fasta file or something else? Do you have any othe suggestions on how to solve that problem? Any insights or suggestions on how to address this issue would be greatly appreciated.
Thank you in advance.
yep
$ samtools faidx hg38.fasta "chr1:121907777-121907777"
>chr1:121907777-121907777
N
it depends of your downstream analysis....
Also, originally I used bcftools query -f '[%CHROM\t%POS\t%REF\t%ALT\n]' inputvcf.g.vcf.gz|grep -v -E '[ACTG]' | head -n 10 for detecting missing values in my REF-Colums.
I am not sure if all missing values in REF are labeled as N. Are N the missing values, or are there additional missing values that my code cannot detect?
Is there an existing function for detecting missing values in REF and ALT?
bcftools norm --check-ref w --fasta-ref in.fa
thank you that works, but I was wondering how to save the result of the analysis and save it to a txt-file
I use the following code to extract the result:
grep "Lines total/split/realigned/skipped"
Is there a better way?
I also can´t save the result I grep in a file.
I Tried the following:
>> missing_data.txt
I also tried tree, > and 2>&1.
Nothing worked.
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cross posted : https://stackoverflow.com/questions/77880020/
Thanks to Pierre for finding the cross-post
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