Incorrect depth from ivar variants reported in variants long table

[wutron]

Description of the bug

When read depth is very high, ivar variants outputs depth in scientific notation. variants_long_table reports only the part of the number before the decimal, resulting in inaccurate depths and allele frequencies.

I believe the issue can be resolved by modifying https://github.com/nf-core/viralrecon/blob/master/bin/ivar_variants_to_vcf.py#L123 to INFO = f"DP={int(float(line[11]))}" to always report depth in vcf as an integer.

$ grep 'e+' out/variants/ivar/ww.tsv

REGION	POS	REF	ALT	REF_DP	REF_RV	REF_QUAL	ALT_DP	ALT_RV	ALT_QUAL	ALT_FREQ	TOTAL_DP	PVAL	PASS	GFF_FEATURE	REF_CODON	REF_AA	ALT_CODON	ALT_AA
MN908947.3	21730	A	G	1317930	667938	35	14947	7521	36	0.0112138	1.33291e+06	0	TRUE	cds-QHD43416.1	TTA	L	TTG	L
MN908947.3	22583	G	+T	1474471	730754	36	79562	0	20	0.0531601	1.49665e+06	0	TRUE	NA	NA	NA	NA	NA
MN908947.3	22977	T	C	1910409	57949	36	87378	1674	36	0.0437341	1.99794e+06	0	TRUE	cds-QHD43416.1	ATC	I	ACC	T
MN908947.3	23052	T	A	1983145	60241	36	12052	145	36	0.0060397	1.99546e+06	0	TRUE	cds-QHD43416.1	TTC	F	TAC	Y
MN908947.3	23126	G	A	3716960	1840637	37	5148	2450	36	0.00138304	3.72223e+06	1.39735e-52	TRUE	cds-QHD43416.1	GCA	A	ACA	T
MN908947.3	23256	T	C	2436217	1880072	36	4472	348	36	0.00183214	2.44086e+06	8.3265e-135	TRUE	cds-QHD43416.1	TTT	F	TCT	S
MN908947.3	24223	C	+T	1600383	258881	36	9068	0	20	0.00566151	1.60169e+06	1	FALSE	NA	NA	NA	NA	NA
MN908947.3	24419	A	G	2602143	1303101	37	3394	1760	35	0.00130258	2.6056e+06	9.93939e-25	TRUE	cds-QHD43416.1	AAC	N	GAC	D
MN908947.3	24442	C	A	1274046	1271015	36	36373	36310	36	0.0277556	1.31047e+06	0	TRUE	cds-QHD43416.1	AAC	N	AAA	K
MN908947.3	24516	A	G	3613820	1381048	37	3692	218	36	0.00102047	3.61794e+06	0.192741	FALSE	cds-QHD43416.1	GAC	D	GGC	G

$ awk -F, '$10>1' out/variants/ivar/variants_long_table.csv

SAMPLE	CHROM	POS	REF	ALT	FILTER	DP	REF_DP	ALT_DP	AF	GENE	EFFECT	HGVS_C	HGVS_P	HGVS_P_1LETTER	CALLER
ww	MN908947.3	21730	A	G	PASS	1	1317930	14947	14947.0	S	synonymous_variant	c.168A>G	p.Leu56Leu	p.L56L	ivar
ww	MN908947.3	22583	G	GT	PASS	1	1474471	79562	79562.0	S	frameshift_variant&stop_gained	c.1026dupT	p.Asn343fs	p.N343fs	ivar
ww	MN908947.3	22977	T	C	PASS	1	1910409	87378	87378.0	S	missense_variant	c.1415T>C	p.Ile472Thr	p.I472T	ivar
ww	MN908947.3	23052	T	A	PASS	1	1983145	12052	12052.0	S	missense_variant	c.1490T>A	p.Phe497Tyr	p.F497Y	ivar
ww	MN908947.3	23126	G	A	PASS	3	3716960	5148	1716.0	S	missense_variant	c.1564G>A	p.Ala522Thr	p.A522T	ivar
ww	MN908947.3	23256	T	C	PASS	2	2436217	4472	2236.0	S	missense_variant	c.1694T>C	p.Phe565Ser	p.F565S	ivar
ww	MN908947.3	24223	C	CT	ft	1	1600383	9068	9068.0	S	frameshift_variant	c.2664dupT	p.Gly889fs	p.G889fs	ivar
ww	MN908947.3	24419	A	G	PASS	2	2602143	3394	1697.0	S	missense_variant	c.2857A>G	p.Asn953Asp	p.N953D	ivar
ww	MN908947.3	24442	C	A	PASS	1	1274046	36373	36373.0	S	missense_variant	c.2880C>A	p.Asn960Lys	p.N960K	ivar
ww	MN908947.3	24516	A	G	ft	3	3613820	3692	1230.67	S	missense_variant	c.2954A>G	p.Asp985Gly	p.D985G	ivar

Command used and terminal output

No response

Relevant files

No response

System information

Nextflow version: 19.01.0.5050
Hardware: Cloud VM
Executor: local
Container engine: Docker
OS: Linux
Version of nf-core/viralrecon: 2.5

[drpatelh]

Thanks for reporting @wutron ! Fancy creating a PR with a fix for this issue and #369 ? Your timing is great because I am planning to release tomorrow.

[drpatelh]

Fixed in #370

Invited you to become a member of the nf-core Github org too. Thanks for providing the fix! Fancy reviewing and approving the PR? You will be able to test dev once that PR is merged to confirm everything is ok.

nextflow pull nf-core/viralrecon -r dev
nextflow run nf-core/viralrecon <YOUR_PARAMETERS> -r dev