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convert GT:PL format to GT:GP format

Currently you have phred-scaled genotype likelihoods or PL values. Genotype likelihoods give the likelihood of observing the read data (i.e. the number of reads which map to either the ref or alt ...
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2 votes

need bam file for pilon

Run a short-read mapper. For example: bwa index assembled.fasta bwa mem -pt16 assembled.fasta read1.fq.gz read2.fq.gz \ | samtools sort -m4G -@4 -o align.bam -
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