bcftools mipileup error: format error, unexpected A at line 1
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.
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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