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I re-aligned the [HG002 30x PCR-free WGS BAM from Baid et al](https://console.cloud.google.com/storage/browser/brain-genomics-public/research/sequencing/grch38/bam/novaseq/wgs_pcr_free/30x) against hs…
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The --tab output is a great way to visualize annotated variants, especially due to multiple lines used to represent overlapping transcripts, genes, features, etc, and the many options to control this …
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I am currently doing benchmarking of the VCF files with the gold standard file **HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf**. Whil…
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( bedtools v2.25.0-70-g577fecf )
I try to intersect a vcf.gz with a vcf resulting from another bedtools subtract run
run#1: bedtools intersect -a ${afile} -b ${bfile} > ${outfolder}/common_ab.vcf ; #…
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- build mehari transcript DB (ensembl):
- download cdot for ensembl and grch37 / grch38
- download ensembl FASTA for transcripts
- create / fill seqrepo with ENSEMBL FASTAs
- build…
tedil updated
2 months ago
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Dear developer,
I compared trueset file NA12877.vcf.gz( including SNP and IDNEL variants) with query file(only SNP variants). For the INDEL in summary.csv, there are numbers on TRUTH.TP TRUTH.FN col…
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```
cat 2202415007_hemi.vcf | head
/home/zmvanw01/projects/12-sample-comparison/hifiasm-path/geno_analysis/per_samp/2202415007/change_to_hemi/2202415007_hemi.vcf
=mpileup -B -a QS -Ou -f /home…
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Hi! I tried to use the heatmap function, but it did not work. I am not sure where the distance matrix is supposed to be, but it was in my miniconda3 directory, which I think is weird. Could you also t…
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Hi,
I have used longshot for phasing reads (HP & PS tags), but something weird is happening. The genotypes (0|1, 1|0) are switched around in comparison with what I see in IGV.
In IGV, haplotype 1 …
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Dear,
I created the SNP index based on the vcf file of dbSNP156.
An error occurs when performing SNP comparison:
```mrsfast --search hg38.fa --seq ./test/rfx5.fa --threads 6 -e 100 --disable-sam-…