Why Isn'T Na12878 In All.2Of4Intersection.20100804.Genotypes.Vcf.Gz

Question

[Jeremy Leipzig]

these are the samples I see in this this file.

['HG00098', 'HG00100', 'HG00106', 'HG00112', 'HG00114', 'HG00116', 'HG00117', 'HG00118', 'HG00119', 'HG00120', 'HG00122', 'HG00123', 'HG00124', 'HG00126', 'HG00131', 'HG00141', 'HG00142', 'HG00143', 'HG00144', 'HG00145', 'HG00146', 'HG00147', 'HG00148', 'HG00149', 'HG00150', 'HG00151', 'HG00152', 'HG00153', 'HG00156', 'HG00158', 'HG00159', 'HG00160', 'HG00171', 'HG00173', 'HG00174', 'HG00176', 'HG00177', 'HG00178', 'HG00179', 'HG00180', 'HG00181', 'HG00182', 'HG00183', 'HG00185', 'HG00186', 'HG00187', 'HG00188', 'HG00189', 'HG00190', 'HG00231', 'HG00239', 'HG00242', 'HG00243', 'HG00244', 'HG00245', 'HG00247', 'HG00258', 'HG00262', 'HG00264', 'HG00265', 'HG00266', 'HG00267', 'HG00269', 'HG00270', 'HG00272', 'HG00306', 'HG00308', 'HG00311', 'HG00312', 'HG00357', 'HG00361', 'HG00366', 'HG00367', 'HG00368', 'HG00369', 'HG00372', 'HG00373', 'HG00377', 'HG00380', 'HG00403', 'HG00404', 'HG00406', 'HG00407', 'HG00445', 'HG00446', 'HG00452', 'HG00457', 'HG00553', 'HG00554', 'HG00559', 'HG00560', 'HG00565', 'HG00566', 'HG00577', 'HG00578', 'HG00592', 'HG00593', 'HG00596', 'HG00610', 'HG00611', 'HG00625', 'HG00626', 'HG00628', 'HG00629', 'HG00634', 'HG00635', 'HG00637', 'HG00638', 'HG00640', 'NA06984', 'NA06985', 'NA06986', 'NA06989', 'NA06994', 'NA07000', 'NA07037', 'NA07048', 'NA07051', 'NA07056', 'NA07346', 'NA07347', 'NA07357', 'NA10847', 'NA10851', 'NA11829', 'NA11830', 'NA11831', 'NA11832', 'NA11840', 'NA11843', 'NA11881', 'NA11892', 'NA11893', 'NA11894', 'NA11918', 'NA11919', 'NA11920', 'NA11930', 'NA11931', 'NA11932', 'NA11933', 'NA11992', 'NA11993', 'NA11994', 'NA11995', 'NA12003', 'NA12004', 'NA12005', 'NA12006', 'NA12043', 'NA12044', 'NA12045', 'NA12046', 'NA12058', 'NA12144', 'NA12154', 'NA12155', 'NA12156', 'NA12249', 'NA12272', 'NA12273', 'NA12275', 'NA12287', 'NA12340', 'NA12341', 'NA12342', 'NA12347', 'NA12348', 'NA12383', 'NA12399', 'NA12400', 'NA12413', 'NA12414', 'NA12489', 'NA12546', 'NA12716', 'NA12717', 'NA12718', 'NA12749', 'NA12750', 'NA12751', 'NA12761', 'NA12762', 'NA12763', 'NA12775', 'NA12776', 'NA12777', 'NA12778', 'NA12812', 'NA12813', 'NA12814', 'NA12815', 'NA12828', 'NA12830', 'NA12872', 'NA12873', 'NA12874', 'NA12889', 'NA12890', 'NA18486', 'NA18487', 'NA18489', 'NA18498', 'NA18499', 'NA18501', 'NA18502', 'NA18504', 'NA18505', 'NA18507', 'NA18508', 'NA18510', 'NA18511', 'NA18516', 'NA18517', 'NA18519', 'NA18520', 'NA18522', 'NA18523', 'NA18525', 'NA18526', 'NA18527', 'NA18532', 'NA18535', 'NA18537', 'NA18538', 'NA18539', 'NA18541', 'NA18542', 'NA18545', 'NA18547', 'NA18550', 'NA18552', 'NA18553', 'NA18555', 'NA18558', 'NA18560', 'NA18561', 'NA18562', 'NA18563', 'NA18564', 'NA18565', 'NA18566', 'NA18567', 'NA18570', 'NA18571', 'NA18572', 'NA18573', 'NA18574', 'NA18576', 'NA18577', 'NA18579', 'NA18582', 'NA18592', 'NA18593', 'NA18603', 'NA18605', 'NA18608', 'NA18609', 'NA18611', 'NA18612', 'NA18614', 'NA18615', 'NA18616', 'NA18617', 'NA18618', 'NA18619', 'NA18620', 'NA18621', 'NA18622', 'NA18623', 'NA18624', 'NA18625', 'NA18626', 'NA18627', 'NA18628', 'NA18630', 'NA18631', 'NA18632', 'NA18633', 'NA18634', 'NA18636', 'NA18638', 'NA18640', 'NA18642', 'NA18643', 'NA18745', 'NA18853', 'NA18856', 'NA18858', 'NA18861', 'NA18867', 'NA18868', 'NA18870', 'NA18871', 'NA18873', 'NA18874', 'NA18907', 'NA18908', 'NA18909', 'NA18910', 'NA18912', 'NA18916', 'NA18940', 'NA18941', 'NA18942', 'NA18943', 'NA18944', 'NA18945', 'NA18947', 'NA18948', 'NA18949', 'NA18950', 'NA18951', 'NA18952', 'NA18953', 'NA18955', 'NA18956', 'NA18959', 'NA18960', 'NA18961', 'NA18963', 'NA18964', 'NA18965', 'NA18967', 'NA18968', 'NA18970', 'NA18971', 'NA18972', 'NA18973', 'NA18974', 'NA18975', 'NA18976', 'NA18977', 'NA18979', 'NA18980', 'NA18981', 'NA18982', 'NA18983', 'NA18984', 'NA18985', 'NA18986', 'NA18987', 'NA18988', 'NA18989', 'NA18990', 'NA18997', 'NA18999', 'NA19000', 'NA19001', 'NA19002', 'NA19003', 'NA19004', 'NA19005', 'NA19007', 'NA19009', 'NA19010', 'NA19012', 'NA19027', 'NA19044', 'NA19054', 'NA19055', 'NA19056', 'NA19057', 'NA19058', 'NA19059', 'NA19060', 'NA19062', 'NA19063', 'NA19064', 'NA19065', 'NA19066', 'NA19067', 'NA19068', 'NA19070', 'NA19072', 'NA19074', 'NA19075', 'NA19076', 'NA19077', 'NA19078', 'NA19079', 'NA19082', 'NA19083', 'NA19084', 'NA19085', 'NA19086', 'NA19087', 'NA19088', 'NA19093', 'NA19098', 'NA19099', 'NA19102', 'NA19107', 'NA19108', 'NA19113', 'NA19114', 'NA19116', 'NA19119', 'NA19129', 'NA19130', 'NA19131', 'NA19137', 'NA19138', 'NA19141', 'NA19143', 'NA19144', 'NA19147', 'NA19152', 'NA19153', 'NA19159', 'NA19160', 'NA19171', 'NA19172', 'NA19184', 'NA19189', 'NA19190', 'NA19200', 'NA19201', 'NA19204', 'NA19206', 'NA19207', 'NA19209', 'NA19210', 'NA19213', 'NA19225', 'NA19235', 'NA19236', 'NA19247', 'NA19248', 'NA19256', 'NA19257', 'NA19311', 'NA19312', 'NA19313', 'NA19314', 'NA19332', 'NA19334', 'NA19338', 'NA19346', 'NA19347', 'NA19350', 'NA19355', 'NA19359', 'NA19360', 'NA19371', 'NA19372', 'NA19375', 'NA19376', 'NA19377', 'NA19379', 'NA19381', 'NA19382', 'NA19383', 'NA19384', 'NA19385', 'NA19390', 'NA19391', 'NA19393', 'NA19394', 'NA19395', 'NA19397', 'NA19398', 'NA19399', 'NA19401', 'NA19404', 'NA19428', 'NA19429', 'NA19434', 'NA19435', 'NA19436', 'NA19437', 'NA19438', 'NA19439', 'NA19440', 'NA19443', 'NA19444', 'NA19445', 'NA19446', 'NA19448', 'NA19449', 'NA19451', 'NA19452', 'NA19453', 'NA19455', 'NA19456', 'NA19457', 'NA19461', 'NA19462', 'NA19463', 'NA19466', 'NA19467', 'NA19469', 'NA19471', 'NA19472', 'NA19473', 'NA19474', 'NA19625', 'NA19648', 'NA19649', 'NA19651', 'NA19652', 'NA19654', 'NA19655', 'NA19658', 'NA19660', 'NA19661', 'NA19678', 'NA19684', 'NA19685', 'NA19700', 'NA19701', 'NA19703', 'NA19704', 'NA19707', 'NA19712', 'NA19713', 'NA19720', 'NA19722', 'NA19723', 'NA19725', 'NA19726', 'NA19818', 'NA19819', 'NA19834', 'NA19835', 'NA19900', 'NA19901', 'NA19904', 'NA19908', 'NA19909', 'NA19914', 'NA19916', 'NA19917', 'NA19920', 'NA19921', 'NA19982', 'NA20414', 'NA20502', 'NA20505', 'NA20508', 'NA20509', 'NA20510', 'NA20512', 'NA20515', 'NA20516', 'NA20517', 'NA20518', 'NA20519', 'NA20520', 'NA20521', 'NA20522', 'NA20524', 'NA20525', 'NA20526', 'NA20527', 'NA20528', 'NA20529', 'NA20530', 'NA20531', 'NA20532', 'NA20533', 'NA20534', 'NA20535', 'NA20536', 'NA20537', 'NA20538', 'NA20539', 'NA20540', 'NA20541', 'NA20542', 'NA20543', 'NA20544', 'NA20581', 'NA20582', 'NA20585', 'NA20586', 'NA20588', 'NA20589', 'NA20752', 'NA20753', 'NA20754', 'NA20755', 'NA20756', 'NA20757', 'NA20758', 'NA20759', 'NA20760', 'NA20761', 'NA20765', 'NA20769', 'NA20770', 'NA20771', 'NA20772', 'NA20773', 'NA20774', 'NA20775', 'NA20778', 'NA20783', 'NA20785', 'NA20786', 'NA20787', 'NA20790', 'NA20792', 'NA20795', 'NA20796', 'NA20797', 'NA20798', 'NA20799', 'NA20800', 'NA20801', 'NA20802', 'NA20803', 'NA20804', 'NA20805', 'NA20806', 'NA20807', 'NA20808', 'NA20809', 'NA20810', 'NA20811', 'NA20812', 'NA20813', 'NA20814', 'NA20815', 'NA20816', 'NA20818', 'NA20819', 'NA20826', 'NA20828']

Where can I find a vcf with this NA12878 and her parents?

[Michael]

Hi Jeremy, this question appears a bit cryptic to me, could you expand it a bit for the sake of searching and others trying to do similar tasks? I guess you are looking for a vcf file for a certain individual in 1kg phase (1,2?) using a file. How do you know that the individual must be there? Where is that file coming from and what kind of information are you showing us here?

[Jeremy Leipzig]

Well I should have probably prefaced it by saying NA12878 is the most cited individual in 1000 Genomes, and that ALL.2of4intersection.20100804.genotypes.vcf.gz (as ungainly as that name is) is arguably the most referenced VCF file in 1000 Genomes (if there is such an award). So I was wondering why I couldn't find her in it, and where I could find her variants, and that of her parents.

[Michael]

Ah, interesting, is this the entry: http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878

Answer 1

[Pierre Lindenbaum]

try:

ftp://ftp.platinumgenomes.org/trio/

and

$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/alignment.index" | grep 12878

and

$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/current.tree" | grep NA12878 | grep -i vcf

[matted]

The Illumina Platinum Genomes site does have VCFs you want, though at a higher coverage (and maybe different centers?) than 1000 Genomes.

As Pierre hints at, you could also download the raw BAMs from 1000 Genomes and do trio-aware SNP calling yourself (a bit tedious, though).

I haven't dug into the documentation enough to verify this, but it appears from spot-checking that all children in trios are not included in the 1000 Genomes ALL*vcf.gz files. I speculate that this is because they want only unrelated samples so that downstream population analyses aren't confounded. Also, the multi-sample SNP calling they use probably has assumptions that are violated when you feed it a handful of parents+children as input.

Answer 2

[Laura]

NA12878 was not part of the phase1 sequencing effort and as such is not part of the official phase1 release nor 20100804 either

It will be part of the phase3 release both as it was used in a subsampled manner in the low coverage calling but also it has new high coverage pcr free sequence along with its parents which was being used for variant calling again