Redundancy in TCGA data

dsmarcoantonio · 04-06-2013, 08:38 AM

maf file in TCGA have redundancy on most genes (See below a example). Can anyone help me in this issue? This is not only in mutation annotation format files but also in RNA-seq to. I don't know what this mean.
Why the same gene is replicated by rows???

Ex:
A4GNT 51146 broad.mit.edu 37 3 137843364 137843364 + Silent SNP T C C TCGA-CJ-4882-01A-02D-1429-08 TCGA-CJ-4882-11A-01D-1429-08 Somatic Phase_I Capture Illumina GAIIx
A4GNT 51146 broad.mit.edu 37 3 137843364 137843364 + Silent SNP T C C TCGA-CJ-4882-01A-02D-1429-08 TCGA-CJ-4882-11A-01D-1429-08 Somatic Phase_I Capture Illumina GAIIx
A4GNT 51146 broad.mit.edu 37 3 137843364 137843364 + Silent SNP T C C TCGA-CJ-4882-01A-02D-1429-08 TCGA-CJ-4882-11A-01D-1429-08 Somatic Phase_I Capture Illumina GAIIx
A4GNT 51146 broad.mit.edu 37 3 137843364 137843364 + Silent SNP T C C TCGA-CJ-4882-01A-02D-1429-08 TCGA-CJ-4882-11A-01D-1429-08 Somatic Phase_I Capture Illumina GAIIx

Thanks a lot

Richard Finney · 04-06-2013, 09:33 AM

There's multiple version of KIRC mafs in various directories.
I'm not sure which one is gospel and which ones are apocryphal.

____ my notes ... _____

-bash-3.00$ grep -n "A4GNT" *.ma* | grep 137843364 | grep "TCGA.CJ.4882" | cut -f1-3
An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf:10685:A4GNT 51146 broad.mit.edu
An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf.1:10685:A4GNT 51146 broad.mit.edu
BI_and_BCM_1.4.aggregated.tcga.somatic.maf:21903:A4GNT 51146 broad.mit.edu
BI_and_BCM_1.4.aggregated.tcga.somatic.maf.1:21903:A4GNT 51146 broad.mit.edu
BI_and_BCM_1.4.aggregated.tcga.somatic.maf.2:21903:A4GNT 51146 broad.mit.edu
BI_and_BCM_1.4.aggregated.tcga.somatic.maf.3:21903:A4GNT 51146 broad.mit.edu
PR_TCGA_KIRC_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf:21924:A4GNT 51146 broad.mit.edu
-bash-3.00$ ls -l An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf
-rw-rw-r-- 1 finneyr finneyr 2703818 Jan 30 2012 An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf
-bash-3.00$ ls -l BI_and_BCM_1.4.aggregated.tcga.somatic.maf
-rw-rw-r-- 1 finneyr finneyr 21113158 Aug 8 2012 BI_and_BCM_1.4.aggregated.tcga.somatic.maf
-bash-3.00$ ls -l BI_and_BCM_1.4.aggregated.tcga.somatic.maf
-rw-rw-r-- 1 finneyr finneyr 21113158 Aug 8 2012 BI_and_BCM_1.4.aggregated.tcga.somatic.maf
-bash-3.00$ ls -l PR_TCGA_KIRC_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf
-rw-rw-r-- 1
finneyr finneyr 32848977 Dec 6 12:10 PR_TCGA_KIRC_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf
-bash-3.00$ grep -n "A4GNT" *.ma* | grep 137843364 | grep "TCGA.CJ.4882" | cut -f1 -d":" | awk '{print "ls -l "$1}' | bash
-rw-rw-r-- 1 finneyr finneyr 2703818 Jan 30 2012 An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf
-rw-rw-r-- 1 finneyr finneyr 3747830 Oct 23 16:24 An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf.1
-rw-rw-r-- 1 finneyr finneyr 21113158 Aug 8 2012 BI_and_BCM_1.4.aggregated.tcga.somatic.maf
-rw-rw-r-- 1 finneyr finneyr 23056811 Oct 19 16:55 BI_and_BCM_1.4.aggregated.tcga.somatic.maf.1
-rw-rw-r-- 1 finneyr finneyr 23056811 Nov 5 12:00 BI_and_BCM_1.4.aggregated.tcga.somatic.maf.2
-rw-rw-r-- 1 finneyr finneyr 23056811 Jan 9 12:48 BI_and_BCM_1.4.aggregated.tcga.somatic.maf.3
-rw-rw-r-- 1 finneyr finneyr 32848977 Dec 6 12:10 PR_TCGA_KIRC_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf

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04-06-2013, 08:38 AM	#1
dsmarcoantonio Junior Member Location: Brazil, Ribeirão Preto Join Date: Sep 2012 Posts: 5	Redundancy in TCGA data maf file in TCGA have redundancy on most genes (See below a example). Can anyone help me in this issue? This is not only in mutation annotation format files but also in RNA-seq to. I don't know what this mean. Why the same gene is replicated by rows??? Ex: A4GNT 51146 broad.mit.edu 37 3 137843364 137843364 + Silent SNP T C C TCGA-CJ-4882-01A-02D-1429-08 TCGA-CJ-4882-11A-01D-1429-08 Somatic Phase_I Capture Illumina GAIIx A4GNT 51146 broad.mit.edu 37 3 137843364 137843364 + Silent SNP T C C TCGA-CJ-4882-01A-02D-1429-08 TCGA-CJ-4882-11A-01D-1429-08 Somatic Phase_I Capture Illumina GAIIx A4GNT 51146 broad.mit.edu 37 3 137843364 137843364 + Silent SNP T C C TCGA-CJ-4882-01A-02D-1429-08 TCGA-CJ-4882-11A-01D-1429-08 Somatic Phase_I Capture Illumina GAIIx A4GNT 51146 broad.mit.edu 37 3 137843364 137843364 + Silent SNP T C C TCGA-CJ-4882-01A-02D-1429-08 TCGA-CJ-4882-11A-01D-1429-08 Somatic Phase_I Capture Illumina GAIIx Thanks a lot

04-06-2013, 09:33 AM	#2
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	There's multiple version of KIRC mafs in various directories. I'm not sure which one is gospel and which ones are apocryphal. ____ my notes ... _____ -bash-3.00$ grep -n "A4GNT" .ma \| grep 137843364 \| grep "TCGA.CJ.4882" \| cut -f1-3 An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf:10685:A4GNT 51146 broad.mit.edu An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf.1:10685:A4GNT 51146 broad.mit.edu BI_and_BCM_1.4.aggregated.tcga.somatic.maf:21903:A4GNT 51146 broad.mit.edu BI_and_BCM_1.4.aggregated.tcga.somatic.maf.1:21903:A4GNT 51146 broad.mit.edu BI_and_BCM_1.4.aggregated.tcga.somatic.maf.2:21903:A4GNT 51146 broad.mit.edu BI_and_BCM_1.4.aggregated.tcga.somatic.maf.3:21903:A4GNT 51146 broad.mit.edu PR_TCGA_KIRC_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf:21924:A4GNT 51146 broad.mit.edu -bash-3.00$ ls -l An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf -rw-rw-r-- 1 finneyr finneyr 2703818 Jan 30 2012 An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf -bash-3.00$ ls -l BI_and_BCM_1.4.aggregated.tcga.somatic.maf -rw-rw-r-- 1 finneyr finneyr 21113158 Aug 8 2012 BI_and_BCM_1.4.aggregated.tcga.somatic.maf -bash-3.00$ ls -l BI_and_BCM_1.4.aggregated.tcga.somatic.maf -rw-rw-r-- 1 finneyr finneyr 21113158 Aug 8 2012 BI_and_BCM_1.4.aggregated.tcga.somatic.maf -bash-3.00$ ls -l PR_TCGA_KIRC_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf -rw-rw-r-- 1 finneyr finneyr 32848977 Dec 6 12:10 PR_TCGA_KIRC_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf -bash-3.00$ grep -n "A4GNT" .ma \| grep 137843364 \| grep "TCGA.CJ.4882" \| cut -f1 -d":" \| awk '{print "ls -l "$1}' \| bash -rw-rw-r-- 1 finneyr finneyr 2703818 Jan 30 2012 An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf -rw-rw-r-- 1 finneyr finneyr 3747830 Oct 23 16:24 An_KIRC_Freeze_1.4_Broad_184_Capture.release.cleaned.maf.1 -rw-rw-r-- 1 finneyr finneyr 21113158 Aug 8 2012 BI_and_BCM_1.4.aggregated.tcga.somatic.maf -rw-rw-r-- 1 finneyr finneyr 23056811 Oct 19 16:55 BI_and_BCM_1.4.aggregated.tcga.somatic.maf.1 -rw-rw-r-- 1 finneyr finneyr 23056811 Nov 5 12:00 BI_and_BCM_1.4.aggregated.tcga.somatic.maf.2 -rw-rw-r-- 1 finneyr finneyr 23056811 Jan 9 12:48 BI_and_BCM_1.4.aggregated.tcga.somatic.maf.3 -rw-rw-r-- 1 finneyr finneyr 32848977 Dec 6 12:10 PR_TCGA_KIRC_PAIR_Capture_All_Pairs_QCPASS.aggregated.capture.tcga.uuid.somatic.maf