REFCODON not consistent with REF

首先使用提供的 GTF、VCF 和 GRCh37 参考 FASTA 重现 predictCoding 调用，然后检查对于列出的位置，报告的 REFCODON 和 VARCODON 与 REF 和 ALT 的关系。将密码子注释与负链 CDS 坐标和 GTF phase 进行比较；当受影响的注释与变异一致，并且回归用例证明修复有效时，即表示完成。

Hello VariantAnnotation team,
I am using the predictCoding function to annotate the coding consequence of SNPs in my VCF file using a custom GTF file. Here is what I ran:

txdb = makeTxDbFromGFF(file="my_genepred.gtf", format="gtf")
fa = open(FaFile("GRCh37.primary_assembly.genome.fa"))
vcf_file = readVcf(file = "my_vcf.vcf")
effects = predictCoding(vcf_file, txdb, fa)

In the result "effects" object, most of the annotation was correct, but some REFCODON or VARCODON were not consistent with REF or ALT. For example, here is the SNP annotation of one gene (I only showed the 'GENEID', "POS", "REFCODON", "VARCODON", "REF", "ALT" columns).

GENEID     POS REFCODON VARCODON REF ALT
ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG 9727738      TGA      TCA   A   G
ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG 9728777      AAA      AAA   C   T
ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG 9728786      AGT      ACT   T   G

You can see that the consequence of A>G mutation if codon TGA>TCA, which doesn't make sense? I went back to my VCF and at chr19:9727738 there is indeed A>G mutation. So it seems that there is a bug of the codon annotation.

I am also attaching the GTF annotation of this gene in case there is problem of my GTF file.
chr19 master_genepred.txt transcript 9720432 9731906 . - . gene_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; transcript_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG";
chr19 master_genepred.txt exon 9720432 9722012 . - . gene_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; transcript_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; exon_number "1"; exon_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG.1";
chr19 master_genepred.txt CDS 9721984 9722012 . - 2 gene_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; transcript_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; exon_number "1"; exon_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG.1";
chr19 master_genepred.txt exon 9727721 9727847 . - . gene_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; transcript_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; exon_number "2"; exon_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG.2";
chr19 master_genepred.txt CDS 9727721 9727847 . - 0 gene_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; transcript_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; exon_number "2"; exon_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG.2";
chr19 master_genepred.txt exon 9728767 9728855 . - . gene_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; transcript_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; exon_number "3"; exon_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG.3";
chr19 master_genepred.txt CDS 9728767 9728799 . - 0 gene_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; transcript_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; exon_number "3"; exon_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG.3";
chr19 master_genepred.txt exon 9730108 9730258 . - . gene_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; transcript_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; exon_number "4"; exon_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG.4";
chr19 master_genepred.txt exon 9731838 9731906 . - . gene_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; transcript_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; exon_number "5"; exon_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG.5";
chr19 master_genepred.txt start_codon 9728797 9728799 . - 0 gene_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; transcript_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; exon_number "3"; exon_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG.3";
chr19 master_genepred.txt stop_codon 9721981 9721983 . - 0 gene_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; transcript_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG"; exon_number "1"; exon_id "ENST00000326044.9_2:chr19:-|22|2017:277:469|truncation|ATG.1";

Thank you!