position mistake of warning?:[warning] found non ACGT ALT character 'N', encoding as 'T' for position: 1547942

[liserjrqlxue]

I use echtvar to encode dbSNP RS ID and got may warns like [warning] found non ACGT ALT character 'N', encoding as 'T' for position: 1547942.
However, I can't found any 'N' at position 1547942.
But before I post an issue, I found that there is a N at position 1547943. This is a bit confusing.

1       1547921 .       CTTTTCTTTTTTTTTTTTTGT   C       .       .       RS=1298430233
1       1547941 .       T       TTC     .       .       RS=1274674348
1       1547942 .       T       TC      .       .       RS=67112328
1       1547942 .       T       C       .       .       RS=140478415
1       1547943 .       T       C       .       .       RS=367618803
1       1547943 .       T       TTN     .       .       RS=1553137706

reproduction

command

echtvar encode debug.zip dbsnp.json debug.vcf.gz

log

[echtvar] adding VCF:debug.vcf.gz
[echtvar] on chromosome "1"
[warning] found non ACGT ALT character 'N', encoding as 'T' for position: 1547942
[echtvar] wrote 28 total variants and 8 long variants (28.57%)

input

debug.zip

dbsnp.json

[
        {"field": "RS",  "alias": "rsID"    }
]

debug.vcf.gz

delete unused contig

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20200501
##source=dbSNP
##dbSNP_BUILD_ID=154
##reference=GRCh37.p13
##phasing=partial
##INFO=<ID=RS,Number=1,Type=Integer,Description="dbSNP ID (i.e. rs number)">
##contig=<ID=1>
##bcftools_normVersion=1.10.2+htslib-1.10.2
##bcftools_normCommand=norm -f GRCh37.p13.fasta.gz -m- -w 10000 -O v GCF_000001405.25.gz; Date=Fri Sep 11 14:51:11 2020
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       1547921 .       CTTTTCTTTTTTTTTTTTTGT   C       .       .       RS=1298430233
1       1547926 .       CTTTTTTTTTT     C       .       .       RS=375755672
1       1547926 .       CTTTTTTT        C       .       .       RS=375755672
1       1547931 .       TTTTTTTTTG      T       .       .       RS=1332647484
1       1547932 .       T       C       .       .       RS=1570432881
1       1547934 .       T       G       .       .       RS=1056143574
1       1547935 .       T       G       .       .       RS=1449414995
1       1547936 .       TTTTG   T       .       .       RS=1305172649
1       1547937 .       T       G       .       .       RS=1375323149
1       1547938 .       T       G       .       .       RS=570290048
1       1547938 .       TTG     T       .       .       RS=1307834628
1       1547939 .       T       C       .       .       RS=140292274
1       1547939 .       T       G       .       .       RS=140292274
1       1547939 .       TG      T       .       .       RS=1285958813
1       1547940 .       G       T       .       .       RS=148775059
1       1547940 .       G       GT      .       .       RS=201873628
1       1547940 .       G       GTT     .       .       RS=201873628
1       1547940 .       G       GTTTTTTT        .       .       RS=201873628
1       1547940 .       G       GTGT    .       .       RS=1557529600
1       1547940 .       G       GTTC    .       .       RS=1557529612
1       1547941 .       T       TTC     .       .       RS=1274674348
1       1547942 .       T       TC      .       .       RS=67112328
1       1547942 .       T       C       .       .       RS=140478415
1       1547943 .       T       C       .       .       RS=367618803
1       1547943 .       T       TTN     .       .       RS=1553137706
1       1547948 .       T       G       .       .       RS=6677572
1       1547948 .       T       TG      .       .       RS=1553137708
1       1547949 .       G       T       .       .       RS=372045450

[brentp]

Hi, here is your problematic variant:

1       1547943 .       T       TTN     .       .       RS=1553137706

note the N in the ALT field. echtvar is reporting the 0-based position. I'll update it to report the 1-based position so there is less confusion.