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Dear all,
Although I already sorted the VCF file according to the chromosome order of the BAM file AND adjusted the header of the VCF file, I still get this error:
" [E:int32_t cmdCramDemuxlet(int…
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I am working on calling variants in spatial transcriptomics data (10x Visium). Since the sequencing depth of spatial transcriptome is poorer than single-cell data, I want to treat all reads in the bam…
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**Is your feature request related to a problem? Please describe.**
VCF preprocessing, currently done by bcftools, requires `##FILTER`, `##FORMAT`, `##INFO`, and `##contig`, which is too strict.
…
arine updated
2 months ago
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Hi @hannespetur,
We ran graphtyper2 using v2.5.1 two years ago to re-genotype SVs.
We noticed that vcf_merge in v2.5.1 does not include the --sv parameter.
Can we still merge the SVs across samp…
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Hi,
```
version: v3.0.1
Files and parameters used:
-e 3000000000
-k 31
-o index/processed
-r chm13v2.0.fa
-t 10
-v merged.sorted.multi.vcf
Determine allele se…
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Hello Nikolaos and Pavlos,
I understand there were issues about Mahattan plots already asked by other ppl. However, I am encoutering something new that others did not mention. I am hoping to get som…
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[1-ERROR]
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CMD: **annotate_with_cravat**: **oc** run \~/Pipline/Hematological_Disease/Fastqs/NDX551335/20240802_E200019755_BeiJingDiAnT7_C_1/00.mergeRawF…
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您好请问您脚本进行bsa分析时在、第二步bsa calculation在运行bsaindex.pl这个脚本时-b1 / -b2 应该输入什么文件呢 我尝试了两个bulk的vcf和包含材料编号的txt文档都会报错,恳请您能指点一下,不胜感激。
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**Describe the bug**
When trying to simulate desired insertions from VCF file, the insertions are not present in the resulting reads. Golden VCF file is completely empty after successful run (no muta…
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Hi developers of `longphase`,
Recently I use `longphase` to phase the ONT sequenced patient data. The phased result looks good but I want to convert the phased VCF to two seperate fasta (one for m…