Calling intervals
By default, ENEO performs variant calling on exons of protein coding genes, with the exception of two types of calling regions:
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Known hard-to-call regions of the human genome. These regions were extensively profiled by the GIAB consortium, and are publicly available. This regions are removed from the VCF file and so are not present in the final VCF output.
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Genes involved in the antigen presentation: given the initial goal of the pipeline to be applied in a personalized cancer vaccine setup, we discared these genes as a source of unwanted variations. We obtained the set of genes using the KEGG pathway annotated as
Expand to see the full set of excluded genes in ENEO
| symbol | description |
|---|---|
| IFNG | interferon gamma |
| TNF | tumor necrosis factor |
| PSME1 | proteasome activator subunit 1 |
| PSME2 | proteasome activator subunit 2 |
| PSME3 | proteasome activator subunit 3 |
| HSPA8 | heat shock protein family A (Hsp70) member 8 |
| HSPA1A | heat shock protein family A (Hsp70) member 1A |
| HSPA1L | heat shock protein family A (Hsp70) member 1 like |
| HSPA1B | heat shock protein family A (Hsp70) member 1B |
| HSPA6 | heat shock protein family A (Hsp70) member 6 |
| HSPA2 | heat shock protein family A (Hsp70) member 2 |
| HSPA4 | heat shock protein family A (Hsp70) member 4 |
| HSP90AA1 | heat shock protein 90 alpha family class A member 1 |
| HSP90AB1 | heat shock protein 90 alpha family class B member 1 |
| HLA-A | major histocompatibility complex, class I, A |
| HLA-B | major histocompatibility complex, class I, B |
| HLA-C | major histocompatibility complex, class I, C |
| HLA-F | major histocompatibility complex, class I, F |
| HLA-G | major histocompatibility complex, class I, G |
| HLA-E | major histocompatibility complex, class I, E |
| HSPA5 | heat shock protein family A (Hsp70) member 5 |
| CANX | calnexin |
| B2M | beta-2-microglobulin |
| PDIA3 | protein disulfide isomerase family A member 3 |
| CALR | calreticulin |
| TAPBP | TAP binding protein |
| TAP1 | transporter 1, ATP binding cassette subfamily B member |
| TAP2 | transporter 2, ATP binding cassette subfamily B member |
| CD8A | CD8 subunit alpha |
| CD8B | CD8 subunit beta |
| CD8B2 | CD8B family member 2 |
| KIR3DL2 | killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 2 |
| KIR3DL1 | killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1 |
| KIR3DL3 | killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 3 |
| KIR3DS1 | killer cell immunoglobulin like receptor, three Ig domains and short cytoplasmic tail 1 |
| KIR2DL2 | killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 2 |
| KIR2DL1 | killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1 |
| KIR2DL3 | killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 3 |
| KIR2DL4 | killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4 |
| KIR2DL5A | killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 5A |
| KLRC1 | killer cell lectin like receptor C1 |
| KLRC2 | killer cell lectin like receptor C2 |
| KLRC3 | killer cell lectin like receptor C3 |
| KLRC4 | killer cell lectin like receptor C4 |
| KLRD1 | killer cell lectin like receptor D1 |
| KIR2DS1 | killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 1 |
| KIR2DS3 | killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 3 |
| KIR2DS4 | killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4 |
| KIR2DS5 | killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 5 |
| KIR2DS2 | killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 2 |
| IFI30 | IFI30 lysosomal thiol reductase |
| LGMN | legumain |
| CTSB | cathepsin B |
| HLA-DMA | major histocompatibility complex, class II, DM alpha |
| HLA-DMB | major histocompatibility complex, class II, DM beta |
| HLA-DOA | major histocompatibility complex, class II, DO alpha |
| HLA-DOB | major histocompatibility complex, class II, DO beta |
| HLA-DPA1 | major histocompatibility complex, class II, DP alpha 1 |
| HLA-DPB1 | major histocompatibility complex, class II, DP beta 1 |
| HLA-DQA1 | major histocompatibility complex, class II, DQ alpha 1 |
| HLA-DQA2 | major histocompatibility complex, class II, DQ alpha 2 |
| HLA-DQB1 | major histocompatibility complex, class II, DQ beta 1 |
| HLA-DRA | major histocompatibility complex, class II, DR alpha |
| HLA-DRB1 | major histocompatibility complex, class II, DR beta 1 |
| HLA-DRB3 | major histocompatibility complex, class II, DR beta 3 |
| HLA-DRB4 | major histocompatibility complex, class II, DR beta 4 |
| HLA-DRB5 | major histocompatibility complex, class II, DR beta 5 |
| CD74 | CD74 molecule |
| CTSL | cathepsin L |
| CTSS | cathepsin S |
| CD4 | CD4 molecule |
| CIITA | class II major histocompatibility complex transactivator |
| RFX5 | regulatory factor X5 |
| RFXANK | regulatory factor X associated ankyrin containing protein |
| RFXAP | regulatory factor X associated protein |
| CREB1 | cAMP responsive element binding protein 1 |
| NFYA | nuclear transcription factor Y subunit alpha |
| NFYB | nuclear transcription factor Y subunit beta |
| NFYC | nuclear transcription factor Y subunit gamma |
Generate a custom interval set
To build a custom set of intervals from a GTF file (here referred to as genecode.gtf.gz), you need to have tabix and bgzip installed. If you built a conda environment for the setup using the setup_env.yml file, tabix and bgzip will be present.
zgrep "protein_coding" gencode.gtf.gz | awk -F'\t' '{ if ($3 == "exon") print $1, $2, $3}' OFS='\t' - | bgzip -c > calling_intervals.BED.gz &&\
tabix -p bed calling_intervals.BED.gz
Then you can use the calling_intervals.BED.gz file as the input for the variant calling step, by putting it in the config_main.yaml