Impute from VCF

docs/imputation_vcf.md

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+Process for imputing from a VCF file
+This is beta code that has not been fully tested
+
+The imputation steps are the same as imputing from a fastq file except instead of calling map-reads you should call map-reads-vcf
+
+* phg map-reads-vcf \
+--hvcf-dir /my/hvcf/dir \
+--index /my/index/dir/myindex.fmd \
+--key-file /my/path/keyfile \
+--output-dir /my/mapping/dir
+
+Example commands
+
+* ./phg map-reads-vcf \
+--hvcf-dir output/vcf_files \
+--index output/index_files/myindex.fmd \
+--key-file data/key_files/read_mapping_data.txt \
+--output-dir output/read_mappings
+
+--hvcf-dir - the directory containing the hVCF files.
+
+--key-file - a tab-delimited list of files
+In the above example, I have made a keyfile and placed it in a subdirectory under the data folder called key_files.
+My example keyfile would look like the following:
+sampleName  filename  filename2
+project reference/iwgsc_refseqv2.1_assembly.fa  vcf/TCAP90K_NAMparents_panel-strand.vcf
+
+--output-dir - the directory to place the read-mapping files.
+
+--index - the ropeBWT3 index file created by the ropebwt-index command.
+
+* Detailed explanation
+
+The VCF file should be aligned to the reference genome so that the ref column matches the reference assembly.
+Multi-allelic SNPs are not supported at this time
+A fastq file is generated for each sample in the VCF file and saved into a fastq directory under the output directory. The length of the fastq reads has been hard coded to 200 bases which works well with wheat. 
+Then ropebwt3 is called to map each of the sample fastq files.
+
+* Performance
+
+Converting a 90K Illumina array VCF file for 150 samples to fastq files takes 1-2 minutes.
+Mapping the fastq file takes about 1 minute per sample.
+