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Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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experiment with coverage cap in collecthsmetrics #98

Closed Kurt-Hetrick closed 4 years ago

Kurt-Hetrick commented 4 years ago

it might be capping median coverage which we don't want

Kurt-Hetrick commented 4 years ago

added to pipeline but need to update cmg and holland samples that had been processed before the fix.

Kurt-Hetrick commented 4 years ago

and unintended consequences...if you set the cap to a depth of 1,000,000, then you get a report with over 1 millions records in it which makes each report about 10 Mb...so yeah, need to come up with a more reasonable threshold...look at the max depth for peters and then go over that some number.

Kurt-Hetrick commented 4 years ago

checked several projects after the switch to 1,000,000 and 32,000 was the highest seen (Peters) so changing it to 75,000 should give plenty of wiggle room while keeping the report file size small

Kurt-Hetrick commented 4 years ago

holland is done

Kurt-Hetrick commented 4 years ago

M_Valle_BH8329_SeqWholeExome_112818_2 is done

Kurt-Hetrick commented 4 years ago

M_Valle_MD_SeqWholeExome_120417_3 is done

Kurt-Hetrick commented 4 years ago

M_Valle_MD_SeqWholeExome_120417_1_GRCh38 is done

Kurt-Hetrick commented 4 years ago

M_Valle_MD_SeqWholeExome_120417_2_GRCh38 is done

Kurt-Hetrick commented 4 years ago

M_Valle_BH8329_SeqWholeExome_112818_2_GRCh38 is done

Kurt-Hetrick commented 4 years ago

Peters_CRC_SeqCustom_020317_1 is done

Kurt-Hetrick commented 4 years ago

done