🧬 Lancet padding vaf #12
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added 2 commits
April 21, 2020 23:30
migbro
requested changes
Apr 22, 2020
| @@ -21,6 +21,14 @@ Each VCF file run at every padding/window length was used to run consensus(sam | |||
| - `results/all_samples_consensus_comparisons` - This file has variant numbers and also annotations/locations of where the missing variants are | |||
| - `results/var_comparison.pn` | |||
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| 3. Comparing variant allele frequencies | |||
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| Variant allele frequencies between different padding values is compared using lancet VCF files. Variant allele frequencies are calculated from the VCF files using (alt allele DP/total DP from tumor sample). Violin plots below show that the VAF do not vary between different padding lengths except for 75-100 | |||
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"padding and window size combinations"
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Thanks! resolved in the commit below
migbro
approved these changes
Apr 22, 2020
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Added variant allele frequencies plots and updated README for lancet padding analysis
Result plot -
results/variant_allele_frequencies.pngCode updated -
VAF_plots.ipynbTicket here