RFE Picard CollectWgsMetrics: allow reporting coverage between 0 and 1X
Hello,
I would file an issue on GitHub directly, but I saw the guidelines ask first to post here. For the record, this isn't a support question but a request for an enhancement (RFE).
Currently CollectWgsMetrics will report a coverage of 0 if the coverage is < 1. However, there are specific use cases, like shallow whole genome sequencing (sWGS, also called ultra low-pass whole genome sequencing or ULP-WGS) where the coverage ranges between 0.1X and 1X. Knowing the exact coverage is important for some downstream applications.
Hence it would be useful to have Picard support coverages < 1X.
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Thank you for this suggestion. Feature requests are frequently added to the list of enhancements planned. In the mean time we recommend using
samtools coverage
to calculate the depth of low coverage whole genome sequencing samples as that tool comprehensively provides per contig mean depth and coverage in both tabular format and histogram format. Below are 2 examples
#rname startpos endpos numreads covbases coverage meandepth meanbaseq meanmapq
chr1 1 248956422 4173570 125519389 50.4182 0.83681 35.7 34.6
chr2 1 242193529 4065424 132785848 54.8263 0.837859 35.7 39
chr3 1 198295559 3448985 109924141 55.4345 0.86756 35.7 39.3
chr4 1 190214555 3356811 106522794 56.0014 0.880106 35.6 38.6
chr5 1 181538259 3044848 99150981 54.6171 0.837234 35.7 39.1
chr6 1 170805979 2896593 94502040 55.3271 0.846693 35.7 39.4
chr7 1 159345973 2636887 86517254 54.2952 0.825836 35.7 37.6
chr8 1 145138636 2454186 79838449 55.0084 0.844026 35.7 39.1
chr9 1 138394717 2020200 65992796 47.6845 0.728653 35.7 35.8
chr10 1 133797422 2264592 72248216 53.9982 0.843677 35.8 37.7
chr11 1 135086622 2217387 72641324 53.7739 0.819415 35.8 38.1
chr12 1 133275309 2199192 72431642 54.3474 0.823743 35.7 39
chr13 1 114364328 1796379 55362183 48.4086 0.784253 35.7 37.2
chr14 1 107043718 1478855 48386890 45.2029 0.689157 35.7 39.2
chr15 1 101991189 1383026 45622715 44.732 0.676917 35.8 36.7
chr16 1 90338345 1473930 42497170 47.0422 0.813445 35.8 32.3
chr17 1 83257441 1260033 41938618 50.3722 0.754178 35.9 35.7
chr18 1 80373285 1375723 44480961 55.343 0.854435 35.7 37.5
chr19 1 58617616 738695 25876488 44.1446 0.628603 36 36.2
chr20 1 64444167 1081179 34185392 53.0465 0.836141 35.9 35.9
chr21 1 46709983 737164 20895119 44.7337 0.785525 35.8 32.4
chr22 1 50818468 609194 18905686 37.2024 0.596401 35.9 32.3
chrX 1 156040895 2549979 84348437 54.0553 0.815987 35.7 37
chrY 1 57227415 102443 2025053 3.53861 0.0845978 35.8 7.53chr1 (248.96Mbp)
> 78.38% | : | Number of reads: 4173570
> 69.67% | :: |
> 60.96% | :: | Covered bases: 125.52Mbp
> 52.25% | ... ............................................. . ...... :: .. .. .. ............... ................. .. ......... . .. .... . | Percent covered: 50.42%
> 43.54% | .:.::....:.::.:.:... .::.:::.:::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:: ::::::.::...::::::::::::::::::::::::::::::::::::::.::::::::::::::::::.:.:.:::::::::::::::::| Mean coverage: 0.837x
> 34.83% |..:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::| Mean baseQ: 35.7
> 26.13% |:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::| Mean mapQ: 34.6
> 17.42% |:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::|
> 8.71% |:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::| Histo bin width: 1.16Mbp
> 0.00% |:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::| Histo max bin: 87.084%
1 11.63M 23.27M 34.90M 46.53M 58.17M 69.80M 81.43M 93.07M 104.70M 116.33M 127.97M 139.60M 151.24M 162.87M 174.50M 186.14M 197.77M 209.40M 221.04M 232.67M 248.96M
chr2 (242.19Mbp)
> 53.25% | ... ...... . . .... :: .. .:......::. .. .: ......... . :. . ... .. .... .... .........::.::......:......:.:::... ........:..::.....:...... :.. ...::.. .:....... | Number of reads: 4065424
> 47.33% |:..:::::..::::::::::::..:::::::::::::::::::::::::::::::::::::::::.:::::::::.::. :: :..:::::::::::::::::::.:::::..:.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::. ::::::::::..::::. |
> 41.42% |:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::. :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::| Covered bases: 132.79Mbp
> 35.50% |:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::| Percent covered: 54.83%
> 29.58% |:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::| Mean coverage: 0.838x
> 23.67% |:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::| Mean baseQ: 35.7
> 17.75% |:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::| Mean mapQ: 39
> 11.83% |::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::|
> 5.92% |::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::| Histo bin width: 1.13Mbp
> 0.00% |::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::| Histo max bin: 59.166%
1 11.32M 22.63M 33.95M 45.27M 56.59M 67.90M 79.22M 90.54M 101.86M 113.17M 124.49M 135.81M 147.13M 158.44M 169.76M 181.08M 192.40M 203.71M 215.03M 226.35M 242.19MI hope this helps.
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