Qihan Long
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Activity overview
Latest activity by Qihan Long-
Qihan Long commented,
Hi Genevieve Brandt, I got it! Thanks for your clarification, it's of great help~
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Qihan Long commented,
Hi Genevieve Brandt, Thank you for your timely update, I successfully removed the annotation using GATK's SelectVariants with --drop-info-annotation option which proved GATK's versatility~ Unfortu...
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Qihan Long commented,
FYI, if anyone wants to utilize PyVCF to read in vcf records I mentioned before, you'll definitely found the error "ValueError: could not convert string to float: '167|35|14" which means PyVCF cann...
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Qihan Long commented,
Hi Genevieve, Thanks for your time~ Much appreciated!
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Qihan Long commented,
Thanks for your instant reply and inspection! I shall try to use Mutect2 (4.2.0.0) combined with FilterMutectCalls (4.1.6.0) to finish my variant calling and annotation process. Hope it's a bug wit...
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Qihan Long commented,
Hi, actually I changed all the separators within "AS_UNIQ_ALT_READ_COUNT=167|35|14" from "|" into "," and used "AS_UNIQ_ALT_READ_COUNT=167,35,14" as input records. Then the error has disappeared, w...
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Qihan Long created a post,
The output of Mutect2 cannot be accepted by FilterMutectCalls in GATK-4.2.0.0
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.2.0.0b) Exact command used: gatk FilterMutectCalls \-R /public1/data/resources/ref_genome/GRCh38/GRCh38.d1.vd1.fa \-V...
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Qihan Long commented,
Hi, nice documentation, but the demo commands have a minor problem VariantAnnotator \ -R reference.fasta \ -I input.bam \ -V input.vcf \ -o output.vcf \ -A Coverage \ --dbsnp d...