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docs/pipeline.md

@@ -68,7 +68,7 @@ If a map file is available (currently TOPMed only), the following cmd is execute
 --format GT,DS,GP --allTypedSites --meta --minRatio 0.00001 --referenceEstimates --map B38_MAP_FILE.map
 ````
 
-## HLA imputation pipeline
+## HLA Imputation Pipeline
 
 In addition to intergenic SNPs, HLA imputation outputs five different types of markers: (1) binary marker for classical HLA alleles; (2) binary marker for the presence/absence of a specific amino acid residue; (3) HLA intragenic SNPs, and (4) binary markers for insertion/deletions, as described in the typical output below. The goal is to minimize prior assumption on which types of variations will be causal and test all types of variations simultaneously in an unbiased fashion. However, the users are always free to restrict analyses to specific marker subsets.
 
@@ -78,7 +78,7 @@ In addition to intergenic SNPs, HLA imputation outputs five different types of m
 
 | Type   |      Format      |  Example |
 |----------|-------------|------|
-| Classical HLA alleles |  HLA\_[GENE]*[ALLELE]| HLA_A*01:02 (two-field allele) <br> HLA_A*02 (one-field allele) |
+| Classical HLA alleles |  HLA\_[GENE]\*[ALLELE]| HLA_A\*01:02 (two-field allele) <br> HLA_A\*02 (one-field allele) |
 | HLA amino acids |  AA_[GENE]\_[AMINO ACID POSITION]\_[GENOMIC POSITION]\_[EXON]\_[RESIDUE] | AA_B_97_31324201_exon3_V (amino acid position 97 in HLA-B, genomic position 31324201 (GrCh37) in exon 3, residue = V (Val) ) |
 | HLA intragenic SNPs |  SNPS_[GENE]\_[GENE POSITION]\_[GENOMIC POSITION]\_[EXON/INTRON] | SNPS_C_2666_31237183_intron6 (SNP at position 2666 of the gene body, genomic position 31237183 in intron 6)|
 | Insertions/deletions |  INDEL_[TYPE]\_[GENE]\_[POSITION]| INDEL_AA_C_300x301_31237792 Indel between amino acids 300 and 301 in HLA-C, at genomic position 31237792) |