GoNL aligned sequence data in BAM format.

We mapped the data to the UCSC human reference genome build 37 using BWA 0.5.9-r16. We first mapped each read pair separately using bwa aln. Then we used bwa sampe to map the paired reads together to a BAM9 file. The BAM file was then sorted by genomic position and indexed using PicardTools-1.32 SortSam. To prevent PCR artifacts from influencing the downstream analysis of our data, we used Picard to mark the duplicate reads, which were ignored in downstream analysis. We used GATK IndelRealigner on our data around known indels (from 1KG Pilot). The IndelRealigner creates all possible read alignments using the source and computes the likelihood of the data containing the indel based on the read pileup. Whenever the maximum likelihood contains an indel, the reads are realigned accordingly. Each base is associated with a phred-scaled base quality score. Calibration of Phred scores is crucial as they are used in some of the downstream analysis models. We used GATK to recalibrate the base qualities with respect to (i) the base cycle, (ii) original quality score, and (iii) dinucleotide context. To minimize issues stemming from mapping problems around indels, we decided to undergo a second round of indel realignment using the GATK IndelRealigner by family rather than by individual. For this second round, we considered two sources of possible indels: 1KG Phase 1 indels and indels aligned by BWA in the GoNL data.

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Studies are experimental investigations of a particular phenomenon. e.g. case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients. Click on one of the Study IDs below to find out more.

Study ID Study Title Study Type
EGAS00001000644 Other
ID File Type Size Located in Quality Control
EGAF00000583426 bam 178.9 GB
EGAF00000583427 bam 166.6 GB
EGAF00000583428 bam 167.8 GB
EGAF00000583429 bam 181.4 GB
EGAF00000583430 bam 166.5 GB
EGAF00000583431 bam 163.6 GB
EGAF00000583432 bam 176.3 GB
EGAF00000583433 bam 180.9 GB
EGAF00000583434 bam 170.5 GB
EGAF00000583435 bam 222.5 GB
EGAF00000583436 bam 192.0 GB
EGAF00000583437 bam 229.8 GB
EGAF00000583438 bam 199.1 GB
EGAF00000583439 bam 222.3 GB
EGAF00000583440 bam 186.2 GB
EGAF00000583441 bam 186.0 GB
EGAF00000583442 bam 185.9 GB
EGAF00000583443 bam 181.8 GB
EGAF00000583444 bam 184.2 GB
EGAF00000583445 bam 199.0 GB
EGAF00000583446 bam 222.1 GB
EGAF00000583447 bam 206.4 GB
EGAF00000583448 bam 234.4 GB
EGAF00000583449 bam 219.4 GB
EGAF00000583450 bam 173.5 GB
EGAF00000583451 bam 163.8 GB
EGAF00000583452 bam 187.4 GB
EGAF00000583453 bam 211.8 GB
EGAF00000583454 bam 152.8 GB
EGAF00000583455 bam 205.8 GB
EGAF00000583456 bam 185.7 GB
EGAF00000583457 bam 196.7 GB
EGAF00000583458 bam 216.7 GB
EGAF00000583459 bam 175.0 GB
EGAF00000583460 bam 187.6 GB
EGAF00000583461 bam 169.9 GB
EGAF00000583462 bam 188.1 GB
EGAF00000583463 bam 199.8 GB
EGAF00000583464 bam 179.2 GB
EGAF00000583465 bam 190.5 GB
EGAF00000583466 bam 202.1 GB
EGAF00000583467 bam 169.2 GB
EGAF00000583468 bam 200.8 GB
EGAF00000583469 bam 203.3 GB
EGAF00000583470 bam 235.0 GB
EGAF00000583471 bam 238.6 GB
EGAF00000583472 bam 178.5 GB
EGAF00000583473 bam 207.3 GB
EGAF00000583474 bam 227.8 GB
EGAF00000583475 bam 175.5 GB
EGAF00000583476 bam 217.0 GB
EGAF00000583477 bam 177.2 GB
EGAF00000583478 bam 200.3 GB
EGAF00000583479 bam 184.5 GB
EGAF00000583480 bam 214.0 GB
EGAF00000583481 bam 190.8 GB
EGAF00000583482 bam 190.9 GB
EGAF00000583483 bam 224.3 GB
EGAF00000583484 bam 169.4 GB
EGAF00000583485 bam 207.9 GB
EGAF00000583486 bam 222.0 GB
EGAF00000583487 bam 159.3 GB
EGAF00000583488 bam 190.5 GB
EGAF00000583489 bam 200.7 GB
EGAF00000583490 bam 216.9 GB
EGAF00000583491 bam 194.4 GB
EGAF00000583492 bam 170.1 GB
EGAF00000583493 bam 191.9 GB
EGAF00000583494 bam 179.4 GB
EGAF00000583495 bam 176.3 GB
EGAF00000583496 bam 228.0 GB
EGAF00000583497 bam 182.4 GB
EGAF00000583498 bam 189.2 GB
EGAF00000583499 bam 198.5 GB
EGAF00000583500 bam 189.5 GB
EGAF00000583501 bam 203.8 GB
EGAF00000583502 bam 216.2 GB
EGAF00000583503 bam 196.3 GB
EGAF00000583504 bam 223.8 GB
EGAF00000583505 bam 188.7 GB
EGAF00000583506 bam 174.8 GB
EGAF00000583507 bam 205.8 GB
EGAF00000583508 bam 199.3 GB
EGAF00000583509 bam 206.6 GB
EGAF00000583510 bam 202.3 GB
EGAF00000583511 bam 205.9 GB
EGAF00000583512 bam 217.7 GB
EGAF00000583513 bam 161.3 GB
EGAF00000583514 bam 197.1 GB
EGAF00000583515 bam 193.7 GB
EGAF00000583516 bam 180.6 GB
EGAF00000583517 bam 226.3 GB
EGAF00000583518 bam 196.0 GB
EGAF00000583519 bam 180.4 GB
EGAF00000583520 bam 185.1 GB
EGAF00000583521 bam 184.1 GB
EGAF00000583522 bam 190.9 GB
EGAF00000583523 bam 238.5 GB
EGAF00000583524 bam 178.2 GB
EGAF00000583525 bam 185.5 GB
EGAF00000583526 bam 189.3 GB
EGAF00000583527 bam 186.6 GB
EGAF00000583528 bam 203.0 GB
EGAF00000583529 bam 212.8 GB
EGAF00000583530 bam 200.6 GB
EGAF00000583531 bam 168.5 GB
EGAF00000583532 bam 182.9 GB
EGAF00000583533 bam 181.8 GB
EGAF00000583534 bam 216.4 GB
EGAF00000583535 bam 185.9 GB
EGAF00000583536 bam 184.9 GB
EGAF00000583537 bam 187.8 GB
EGAF00000583538 bam 195.6 GB
EGAF00000583539 bam 202.7 GB
EGAF00000583540 bam 185.8 GB
EGAF00000583541 bam 197.9 GB
EGAF00000583542 bam 184.0 GB
EGAF00000583543 bam 225.2 GB
EGAF00000583544 bam 211.3 GB
EGAF00000583545 bam 201.3 GB
EGAF00000583546 bam 188.1 GB
EGAF00000583547 bam 156.7 GB
EGAF00000583548 bam 181.2 GB
EGAF00000583549 bam 180.0 GB
EGAF00000583550 bam 187.5 GB
EGAF00000583551 bam 207.8 GB
EGAF00000583552 bam 189.8 GB
EGAF00000583553 bam 186.0 GB
EGAF00000583554 bam 176.8 GB
EGAF00000583555 bam 192.4 GB
EGAF00000583556 bam 229.2 GB
EGAF00000583557 bam 204.9 GB
EGAF00000583558 bam 177.9 GB
EGAF00000583559 bam 177.4 GB
EGAF00000583560 bam 168.6 GB
EGAF00000583561 bam 169.3 GB
EGAF00000583562 bam 166.8 GB
EGAF00000583563 bam 185.7 GB
EGAF00000583564 bam 192.6 GB
EGAF00000583565 bam 209.2 GB
EGAF00000583566 bam 211.2 GB
EGAF00000583567 bam 185.1 GB
EGAF00000583568 bam 220.3 GB
EGAF00000583569 bam 198.2 GB
EGAF00000583570 bam 184.9 GB
EGAF00000583571 bam 175.3 GB
EGAF00000583572 bam 194.7 GB
EGAF00000583573 bam 207.4 GB
EGAF00000583574 bam 186.3 GB
EGAF00000583575 bam 181.6 GB
EGAF00000583576 bam 193.5 GB
EGAF00000583613 bam 214.3 GB
EGAF00000583614 bam 200.4 GB
EGAF00000583615 bam 189.7 GB
EGAF00000583616 bam 217.6 GB
EGAF00000583617 bam 196.1 GB
EGAF00000583618 bam 209.2 GB
EGAF00000583619 bam 210.7 GB
EGAF00000583620 bam 262.5 GB
EGAF00000583621 bam 188.7 GB
EGAF00000583622 bam 181.0 GB
EGAF00000583623 bam 211.0 GB
EGAF00000583624 bam 183.8 GB
EGAF00000583625 bam 196.3 GB
EGAF00000583626 bam 187.6 GB
EGAF00000583627 bam 163.2 GB
EGAF00000583628 bam 219.1 GB
EGAF00000583629 bam 185.7 GB
EGAF00000583630 bam 187.5 GB
EGAF00000583631 bam 297.5 GB
EGAF00000583632 bam 227.0 GB
EGAF00000606378 bam 214.8 GB
EGAF00000606379 bam 195.2 GB
EGAF00000606380 bam 193.1 GB
EGAF00000606381 bam 262.7 GB
EGAF00000606382 bam 190.0 GB
EGAF00000606383 bam 187.9 GB
EGAF00000606384 bam 206.9 GB
EGAF00000606385 bam 196.9 GB
EGAF00000606386 bam 200.3 GB
EGAF00000606387 bam 212.4 GB
EGAF00000606388 bam 165.4 GB
EGAF00000606389 bam 203.6 GB
EGAF00000606390 bam 189.6 GB
EGAF00000606391 bam 177.7 GB
EGAF00000606392 bam 180.1 GB
EGAF00000606393 bam 207.9 GB
EGAF00000606394 bam 170.7 GB
EGAF00000606395 bam 186.5 GB
EGAF00000606396 bam 293.7 GB
EGAF00000606397 bam 198.7 GB
EGAF00000606398 bam 194.5 GB
EGAF00000606399 bam 209.8 GB
EGAF00000606400 bam 177.0 GB
EGAF00000606401 bam 207.5 GB
EGAF00000606402 bam 234.7 GB
EGAF00000606403 bam 198.8 GB
EGAF00000606404 bam 183.7 GB
EGAF00000606405 bam 204.5 GB
EGAF00000606406 bam 242.7 GB
EGAF00000639388 bam 258.1 GB
EGAF00000639389 bam 275.1 GB
EGAF00000639390 bam 198.8 GB
EGAF00000639391 bam 187.6 GB
EGAF00000639392 bam 210.3 GB
EGAF00000639393 bam 202.7 GB
EGAF00000639394 bam 242.4 GB
EGAF00000639395 bam 223.9 GB
EGAF00000639396 bam 189.0 GB
EGAF00000639397 bam 260.4 GB
EGAF00000639398 bam 191.6 GB
EGAF00000639399 bam 259.6 GB
EGAF00000639400 bam 208.5 GB
EGAF00000639401 bam 188.0 GB
EGAF00000639402 bam 250.3 GB
EGAF00000639403 bam 216.2 GB
EGAF00000639404 bam 271.2 GB
EGAF00000639405 bam 214.7 GB
EGAF00000639406 bam 185.6 GB
EGAF00000639407 bam 193.9 GB
EGAF00000639408 bam 213.5 GB
EGAF00000639409 bam 232.5 GB
EGAF00000639410 bam 295.9 GB
EGAF00000639411 bam 208.9 GB
EGAF00000639412 bam 308.5 GB
EGAF00000639413 bam 206.2 GB
EGAF00000639414 bam 298.5 GB
EGAF00000639415 bam 190.7 GB
EGAF00000639416 bam 197.4 GB
EGAF00000639417 bam 251.2 GB
EGAF00000639418 bam 182.5 GB
EGAF00000639419 bam 281.1 GB
EGAF00000639420 bam 222.4 GB
EGAF00000639421 bam 198.6 GB
EGAF00000639422 bam 202.7 GB
EGAF00000639423 bam 278.1 GB
EGAF00000650094 bam 286.5 GB
EGAF00000650095 bam 318.1 GB
EGAF00000650096 bam 283.7 GB
EGAF00000650097 bam 226.3 GB
EGAF00000650098 bam 211.9 GB
EGAF00000650099 bam 265.8 GB
EGAF00000650100 bam 185.9 GB
EGAF00000650101 bam 204.2 GB
EGAF00000650102 bam 200.6 GB
EGAF00000650103 bam 254.3 GB
EGAF00000650104 bam 242.1 GB
EGAF00000650105 bam 265.1 GB
EGAF00000650106 bam 203.6 GB
EGAF00000654103 bam 208.7 GB
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