katimbach
commented
4 years ago Update: even after reordering my vcf file I am still experiencing the following error: FATAL ERROR - [E:int32_t main(int32_t, char**)] Your VCF/BCF files and SAM/BAM/CRAM files have different ordering of chromosomes. SAM/BAM/CRAM file has 19 before 2, but VCF/BCF file has 19 after 2
However, when I examine the order of the vcf I get:
fileformat=VCFv4.2
fileDate=20200513
source=PLINKv1.90
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional
FORMAT=
CHROM
0 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 3 4 5 6 7 8 9
and when I examine the order of the BAM with samtools I get this: 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9 MT X Y KI270728.1 KI270727.1 KI270442.1 KI270729.1 GL000225.1 KI270743.1 GL000008.2 GL000009.2 KI270747.1 KI270722.1 GL000194.1 KI270742.1 GL000205.2 GL000195.1 KI270736.1 KI270733.1 GL000224.1 GL000219.1 KI270719.1 GL000216.2 KI270712.1 KI270706.1 KI270725.1 KI270744.1 KI270734.1 GL000213.1 GL000220.1 KI270715.1 GL000218.1 KI270749.1 KI270741.1 GL000221.1 KI270716.1 KI270731.1 KI270751.1 KI270750.1 KI270519.1 GL000214.1 KI270708.1 KI270730.1 KI270438.1 KI270737.1 KI270721.1 KI270738.1 KI270748.1 KI270435.1 GL000208.1 KI270538.1 KI270756.1 KI270739.1 KI270757.1 KI270709.1 KI270746.1 KI270753.1 KI270589.1 KI270726.1 KI270735.1 KI270711.1 KI270745.1 KI270714.1 KI270732.1 KI270713.1 KI270754.1 KI270710.1 KI270717.1 KI270724.1 KI270720.1 KI270723.1 KI270718.1 KI270317.1 KI270740.1 KI270755.1 KI270707.1 KI270579.1 KI270752.1 KI270512.1 KI270322.1 GL000226.1 KI270311.1 KI270366.1 KI270511.1 KI270448.1 KI270521.1 KI270581.1 KI270582.1 KI270515.1 KI270588.1 KI270591.1 KI270522.1 KI270507.1 KI270590.1 KI270584.1 KI270320.1 KI270382.1 KI270468.1 KI270467.1 KI270362.1 KI270517.1 KI270593.1 KI270528.1 KI270587.1 KI270364.1 KI270371.1 KI270333.1 KI270374.1 KI270411.1 KI270414.1 KI270510.1 KI270390.1 KI270375.1 KI270420.1 KI270509.1 KI270315.1 KI270302.1 KI270518.1 KI270530.1 KI270304.1 KI270418.1 KI270424.1 KI270417.1 KI270508.1 KI270303.1 KI270381.1 KI270529.1 KI270425.1 KI270396.1 KI270363.1 KI270386.1 KI270465.1 KI270383.1 KI270384.1 KI270330.1 KI270372.1 KI270548.1 KI270580.1 KI270387.1 KI270391.1 KI270305.1 KI270373.1 KI270422.1 KI270316.1 KI270340.1 KI270338.1 KI270583.1 KI270334.1 KI270429.1 KI270393.1 KI270516.1 KI270389.1 KI270466.1 KI270388.1 KI270544.1 KI270310.1 KI270412.1 KI270395.1 KI270376.1 KI270337.1 KI270335.1 KI270378.1 KI270379.1 KI270329.1 KI270419.1 KI270336.1 KI270312.1 KI270539.1 KI270385.1 KI270423.1 KI270392.1 KI270394.1
It seems that in both cases 19 comes before 2, so I don't understand why this error is still emerging.
hyunminkang
guijie2015
Hello,
I am currently running into a bit of issues running demuxlet*, particularly in regards to the non-uniformity of the BAM and VCF files. I manually created my VCF file from genotyping data from 6 different patients using plink. My BAM files were generated from 10X, and when first trying to feed them into demuxlet I ran into errors due to different chromosome ordering (10X generates lexicographical ordering of chromosomes). I was able to reorder the chromosomes in my vcf file to match using: cat merged_vcf.vcf | awk '$1 ~ /^#/ {print $0;next} {print $0 | "sort -k1,1 -k2,2n"}' > merged_sorted_vcf.vcf
However, looking at the chromosome labels of each file I find that while 10X labels chromosomes as MT, X, Y plink uses 22-26 (http://seqanswers.com/forums/showthread.php?t=70046). Will this pose further issue when trying to run demuxlet? And if so how can I relabel these in my VCF file??