Entering edit mode
10 months ago
jiyoung
▴
20
I had a problem using bcftools. After using the command line(below): there is some error in my results. The error message stated: "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[E::fai_build_core] Format error, unexpected "A" at line 4
Failed to read from standard input: unknown file type"
bcftools mpileup -f A.fasta out.bam | bcftools call -mv -Ob -o out.bcf
there is problem in my index file? i using bwa tool to make index file.
bwa index A.fasta
This is my index file (A.fasta)
Thank you in advance for your help.
bcftools wants an index created with
samtools faidx
(describe the number of chromosomes and the lengths of the fasta lines) , notbwa index
(index for mapping with bwa)i suspect your fasta file is a windows file with CRLF lines. https://en.wikipedia.org/wiki/Newline#Issues_with_different_newline_formats ? if true: https://www.cyberciti.biz/faq/how-to-remove-carriage-return-in-linux-or-unix/
My FASTA file was not downloaded from a database. My fasta file was created by converting a txt file to FASTA format. How can I resolve these problems?
what does that mean ?
see the second link
You can usually fix it with the dos2unix command