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This article introduces the relevant knowledge of "how to install and use freebayes". In the operation of actual cases, many people will encounter such a dilemma, so let the editor lead you to learn how to deal with these situations. I hope you can read it carefully and be able to achieve something!

Freebayes is a snp calling software with high sensitivity and easy to use, so it is very popular.

The installation process of the software is as follows

Git clone-recursive git://github.com/ekg/freebayes.gitcd freebayes/make

After the compilation is successful, the executable file is located in the bin directory. For convenience, you can add the bin directory to the PATH environment variable.

For freebayes, only two input files are needed, one is the fasta file that references the genome, and the other is the bam file generated by the comparison. The basic usage is as follows

Freebayes-f ref.fasta align.bam > var.vcf

The fasta file of the reference genome needs to have an index file with the suffix .fai, which can be built through samtools, as follows

Samtools faidx ref.fasta

If the fasta file you provide does not have a corresponding index, the program will build it automatically. For large reference genomes, it is recommended that the index be built first. The compared bam files can be obtained according to the preprocessing process officially recommended by GATK.

The output is in VCF format, as shown below

Head

# # fileformat=VCFv4.2##fileDate=20180626##source=freeBayes v1.2.0 referencereferenceref.fastaple referenceref.fastaple contigitycommand line = ". / freebayes-- fasta-reference ref.fasta align.bam" # # INFO=

Text

# CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GW1NC_023084.1 107. G T 331.137. AB=0;ABP=0;AC=2;AF=1;AN=2;AO=13;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=3.17734;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=22.627;PAIRED=0.615385;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=423;QR=0;RO=0;RPL=0;RPP=31.2394;RPPR=0;RPR=13;RUN=1;SAF=6;SAP=3.17734;SAR=7;SRF=0;SRP=0;SRR=0;TYPE=snp Technology.illumina=1 GT:DP:AD:RO:QR:AO:QA:GL 1xxxxxxxxxxxxxxxxxx

It has been described in detail in previous articles in VCF format, and the meaning of each field can be referred to the comment information in the header.

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