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AstraZeneca-NGS / VarDictJava

VarDict Java port
MIT License
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Mutation detection failed #362

Open calocean opened 2 years ago

calocean commented 2 years ago

Hi, thanks for your contribution to the variation detection. I am using VarDictJava, and encountering some problems, hoping to get your help. The variant we want is not in the tbl file VarDictJava generates. However, the variant can be seen when I look at the BAM file in IGV. The command I have used: vardict-java --amplicon 12:0.90 -Q 15 -q 10 -th 10 -k 0 -G hg38.fa -f 0.001 -N RD20220422 -b RD20220422.bwa.srt.bam -p amplicon.bed | tee RD20220422.vardict.tbl Comparison of results as the following. vardict_amplicon_variant_detect_fail vardict_amplicon_variant_detect_fail_tbl

PolinaBevad commented 2 years ago

Hi @tegent-gift, Small check: as you are using amplicon mode - are all A bases on chr5:1295135 overlapped with amplicon region by 0.9? What if you decrease overlap fraction?

calocean commented 2 years ago

@PolinaBevad Thanks for your reply. I modified the parameters in steps of 0.1 as you suggested, but still can't get the mutation of G->A. I wonder why VarDictJava thinks this is a false positive. I check the phred of base and mapping quality on chr5:1295135. The quality score is good, and the A base should be considered (see the following figure). If it is convenient for you, you can take a look at the material I provided. Many thanks for your help. base_quality material.zip

calocean commented 2 years ago

@PolinaBevad I forgot to attach my bed file. It is now available. hg38_bed.txt