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C: Why is 0/0 homozygous reference call in VCF useful information?
Answer: snippy error
Answer: TSS of protein coding genes
TSS of protein coding genes
Answer: vcf not indexing
Comment: Hybrid assembly Pacbio- Nanopore
Answer: vg call is time consuming
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Recent Replies
Comment: Variant calling of GBS data
by
analyst
▴ 10
It is still giving same warning java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --fi…
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
dzisis1986
▴ 70
It doesn't make sense how to change the threads and in my case it is not working! What kind of problem is that ? is it related to Amazon to…
Comment: STAR aligner options
by
theophile
• 0
I have finally found out the reason behind this behavior. As [pointed out by dsull][1], the beginning of the alignment of read1 to the rat…
Comment: Variant calling of GBS data
by
analyst
▴ 10
Right Pierre, thanks.
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
remove spaces in expressions. 'MQRankSum<0.4'
Comment: Variant calling of GBS data
by
analyst
▴ 10
![enter image description here][1] [1]: /media/images/710829f2-e4af-4743-a31d-822520b4
Comment: Variant calling of GBS data
by
analyst
▴ 10
Vcf file contains this information ![enter image description here][1] [1]: /media/images/b3f699e5-2dd9-4e08-8f5b-2a716544
Comment: Variant calling of GBS data
by
analyst
▴ 10
Command used : **java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --filter-name "QD_f…
Comment: Variant calling of GBS data
by
analyst
▴ 10
I am using gatK version 4.2.1.0 for variant filtration but it generates following warnings: 14:10:40.970 WARN JexlEngine - ![0,14]: 'Read…
Comment: STAR aligner options
by
dsull
★ 5.6k
In that first link, Dr. Dobin states how such configurations will "split" the reads into pieces -- exactly what I alluded to in my comment.…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you for this advice , but when reading the documentation of split2 I found that it generates multiple files for the same fastq file. …
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
ATpoint
81k
I will delete this as it - obviously - does not belong into this thread.
Comment: STAR aligner options
by
theophile
• 0
I searched the different options to increase the sensitivity. As per `--seedSearchStartLmax`, I found several answer from Alexander Dobin o…
Comment: STAR aligner options
by
theophile
• 0
Sorry, I was a bit confused by the layout, thanks for editing and clarifying!
Answer: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I want to calculate the mismatch rate on base-level, samtools stats in.bam | grep "error rate" | cut -f 2,3 error rate: 2.0…
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