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sigven / cpsr

Cancer Predisposition Sequencing Reporter (CPSR)
https://sigven.github.io/cpsr/
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Column `BP1` can't be converted from character to logical #10

Closed jxshi closed 5 years ago

jxshi commented 5 years ago

Hi,

I was trying to run cpsr but it popped up an error when generating output file. Can you check for me please? Thank you in advance!

2019-05-06 17:15:26 - cpsr-writer - INFO - STEP 4: Generation of output files - Cancer predisposition sequencing report
2019-05-06 09:16:00 [INFO] Excluding 0 variants from non-nuclear chromosomes/scaffolds
2019-05-06 09:16:01 [INFO] Number of PASS variants: 3195
2019-05-06 09:16:01 [INFO] Number of SNVs: 2637
2019-05-06 09:16:01 [INFO] Number of deletions: 296
2019-05-06 09:16:01 [INFO] Number of insertions: 251
2019-05-06 09:16:01 [INFO] Number of block substitutions: 0
2019-05-06 09:16:01 [INFO] Extending annotation descriptions related to UniprotKB/SwissProt protein features
2019-05-06 09:16:03 [INFO] Adding citations/phenotypes underlying GWAS hits (NHGRI-EBI GWAS Catalog)
2019-05-06 09:16:04 [INFO] Extending annotation descriptions related to Database of Curated Mutations (DoCM)
2019-05-06 09:16:04 [INFO] Extending annotation descriptions related to KEGG pathways
2019-05-06 09:16:04 [INFO] Extending annotation descriptions related to ClinVar
2019-05-06 09:16:07 [INFO] Filtering variants against the predefined list of n = 209 cancer predisposition genes
2019-05-06 09:16:07 [INFO] Number of variants within cancer predisposition genes: 2705
2019-05-06 09:16:07 [INFO] Number of coding variants in cancer predisposition genes: 106
2019-05-06 09:16:07 [INFO] Found coding variants in the following cancer predisposition genes: PINK1, SPRTN, ALK, EPCAM, MSH6, ABCB11, PMS1, BARD1, FANCD2, XPC, TGFBR2, POLQ, CASR, DTX3L, GATA2, ATR, KDR, FAT1, PRDM9, MSH3, APC, NSD1, PMS2, EGFR, PRSS1, WRN, DOCK8, MTAP, GALNT12, TSC1, RET, JMJD1C, BMPR1A, MEN1, AIP, CEP57, ATM, RECQL, SH2B3, HNF1A, GJB2, BRCA2, ERCC5, MLH3, TSHR, SERPINA1, BUB1B, FANCI, SLX4, RFWD3, FANCA, TP53, BRCA1, RHBDF2, ELANE, ERCC2, CHEK2, APOBEC3B
2019-05-06 09:16:07 [INFO] Looking up germline variants linked to hereditary cancer-predisposing syndromes/cancer phenotypes
2019-05-06 09:16:08 [INFO] Assignment of variants to tier 1/tier 2/tier 3
2019-05-06 09:16:08 [INFO] TIER 1: Pathogenic variants - cancer_phenotype: n = 0
2019-05-06 09:16:08 [INFO] TIER 1: Pathogenic variants - noncancer_phenotype: n = 1
2019-05-06 09:16:08 [INFO] TIER 2: Likely pathogenic variants - cancer_phenotype: n = 0
2019-05-06 09:16:08 [INFO] TIER 2: Likely pathogenic variants - noncancer_phenotype: n = 0
2019-05-06 09:16:09 [INFO] TIER 3: Variants of uncertain significance - cancer_phenotype: n = 4
2019-05-06 09:16:11 [INFO] TIER 3: Variants of uncertain significance - noncancer_phenotype: n = 3
2019-05-06 09:16:12 [INFO] TIER 3: Other unclassified variants: n = 4
2019-05-06 09:16:12 [INFO] Generating tiered set of result variants for output in tab-separated values (TSV) file
Error in bind_rows_(x, .id) :
  Column `BP1` can't be converted from character to logical
Calls: <Anonymous> ... as.data.frame -> <Anonymous> -> bind_rows_ -> .Call
Execution halted
sigven commented 5 years ago

Hi @jxshi, Thanks for using CPSR! I am in the process of releasing a major upgrade of cpsr. If you can share your VCF with me, I can demonstrate how the new report will look.

best, Sigve

jxshi commented 5 years ago

Here is the link to the vcf file. The download link will be valid for 7 days. Thank you!

Cheers!

sigven commented 5 years ago

@jxshi, (cc @brucemoran)

I have uploaded an example report of your VCF from a CPSR run (v 0.4.0 - soon to be pushed to GitHub) here. Make sure you download the file to view the contents properly (Dropbox cannot show the HTML fully).

PS. CPSR/PCGR is not fond of multiallelic variants (unfortunately a common output by GATK). Ideally these records should be decomposed prior to your run

In summary, the new version of CPSR will

thanks, Sigve

jxshi commented 5 years ago

Hi Sigve,

The new report look fantastic! Thank you for you help!

Looking forward to the new release.

Cheers!

Jianxiang

From: Sigve Nakken notifications@github.com Sent: Tuesday, May 7, 2019 12:30 PM To: sigven/cpsr Cc: Shi, Jianxiang; Mention Subject: Re: [sigven/cpsr] Column BP1 can't be converted from character to logical (#10)

@jxshihttps://github.com/jxshi, (cc @brucemoranhttps://github.com/brucemoran)

I have uploaded an example report of your VCF from a CPSR run (v 0.4.0 - soon to be pushed to GitHub) herehttps://www.dropbox.com/s/se85erm4vs2tnyk/fam3010040.cpsr.grch37.html?dl=0. Make sure you download the file to view the contents properly (Dropbox cannot show the HTML fully).

PS. CPSR/PCGR is not fond of multiallelic variants (unfortunately a common output by GATK). Ideally these records should be decomposed prior to your run

In summary, the new version of CPSR will

thanks, Sigve

- You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/sigven/cpsr/issues/10#issuecomment-490203657, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AG4YXGGB37A7LT3LIULHYBDPUHDFHANCNFSM4HK6MX3Q.