Deep variant generated report.html file how to view in gcp ubuntu environment via google vhrome

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hze...@gmail.com

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Feb 13, 2021, 9:30:00 PM2/13/21

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Dear GCP life sciences team

i have a question as I had run deep variant instance

it generated report in ubuntu gcp environment

HG003.output.g.vcf.gz
HG003.output.g.vcf.gz.tbi
HG003.output.vcf.gz
HG003.output.vcf.gz.tbi
HG003.output.visual_report.html
in addition,I did not find "GRCh38_no_alt_analysis_set.fasta" in any bucket gs:// deepvariant
BIN_VERSION="1.1.0"
BASE="${HOME}/deepvariant-run"
INPUT_DIR="${BASE}/input"
REF="GRCh38_no_alt_analysis_set.fasta"
BAM="HG003.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam"
OUTPUT_DIR="${BASE}/output"
DATA_DIR="${INPUT_DIR}/data"
OUTPUT_VCF="HG003.output.vcf.gz"
OUTPUT_GVCF="HG003.output.g.vcf.gz"

2nd question about variant transforms

what are the main steps of variant transforms

storing raw vcf files

validation of vcf files

loading of vcf files from cloud storage to big query

it displays table

i) what about ti/tv ratio

i have difficulty to find it right

ii) also shed light on flattening of bigquery variants

iii) parsing and annotation of vcf files

i ,ii, iii are optional steps for variant transforms

3rd question is

i am uploading file about 1 gb ,500 mb from my pc to cloud storage bucket but it fails and returns error in contrast i copy large files from one bucket to other it copies fast and successful

4th question

bq ls --format=pretty GOOGLE_CLOUD_PROJECT:BIGQUERY_DATASET

this command work

but this does not

bq show --format=pretty GOOGLE_CLOUD_PROJECT:BIGQUERY_DATASET.BIGQUERY_TABLE

is this is the final result of Variant Transforms or i have to calculate ti/tv ratio ,flattening of biqquery variants nad parsing and annotations

-----------------------------------+-------+--------+-------------------+------------------------------+

+-----------------------------------+-------+--------+-------------------+------------------------------+

| variant_uk_covid2020__sample_info | TABLE | | | |

+-----------------------------------+-------+--------+-------------------+------------------------------+

in the end i will paste out the error

as well

(genomic-analysis-255208)$ bq show --format=pretty genomic-analysis-255208:lineageB_1_1_7.variant_uk_covid2020
BigQuery error in show operation: Not found: Table genomic-analysis-255208:lineageB_1_1_7.variant_uk_covid2020

AND

bq show --format=pretty genomic-analysis-255208:lineageB_1_1_7.variant_uk_covid2020__residual

+-----------------+---------------------------------------+------------+-------------+------------+-------------------+------------------------------+--------+

+-----------------+---------------------------------------+------------+-------------+------------+-------------------+------------------------------+--------+

| 14 Feb 01:34:56 | |- reference_name: string | 24 | 996 | | | start_position, end_position | |

+-----------------+---------------------------------------+------------+-------------+------------+-------------------+------------------------------+--------+

-----------------+----------------------------------+------------+-------------+------------+-------------------+------------------+--------+

+-----------------+----------------------------------+------------+-------------+------------+-------------------+------------------+--------+

| 14 Feb 01:34:53 | |- sample_id: integer | 0 | 0 | | | | |

+-----------------+----------------------------------+------------+-------------+------------+-------------------+------------------+--------+

thanks in advance

haroon zeb

hze...@gmail.com

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Feb 13, 2021, 9:41:12 PM2/13/21

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