Wen-ye Yao
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Activity overview
Latest activity by Wen-ye Yao-
Wen-ye Yao commented,
Hi Anthony: I have posted the log about GATK --hapotypeCaller step. I am unsure if the entire log you mentioned is from the "Star mapping" step or just the GATK program. I post the whole program l...
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Wen-ye Yao commented,
Hi Anthony: Thank you for your comments. I did follow the RNAseq variant detection best practices for my data analysis at the beginning. The following is the complete code I used: After I followed...
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Wen-ye Yao commented,
Hi Anthony Dias-Ciarla : Thank you for your message. I updated the haplotypeCaller part log file in the Post. I hope this is what you want.
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Wen-ye Yao created a post,
The expected variants were not detected for pig RNA-seq by GATK
REQUIRED for all errors and issues: a) GATK version used: v4.1.9b) Exact command used: gatk Haplotype -R Sus_scrofa.fa -I BQSR_SAMEA5337669-STARsorted.bam -O SAMEA5337669.vcf.gz --dont-use-soft-cl...